Inhibitors of Retroviral Replication

ABSTRACT

Methods for preventing or treating retroviral infection, such as human immunodeficiency virus, in vivo utilize transcriptional inhibitory compounds. These include cortistatin A and analogs of the cortistatin family.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the priority of U.S. provisional patentapplication No. 61/431,198 filed Jan. 10, 2011 and entitled “CORTISTATINA IS AN INHIBITOR OF HIV REPLICATION”, which is incorporated herein byreference in its entirety.

FIELD OF THE INVENTION

Embodiments of the invention comprise methods for preventing or treatingretroviral infection, such as human immunodeficiency virus (HIV), humanT-cell leukemia virus (HTLV). Further embodiments comprise compoundswhich modulate Tat-TAR interactions, the functions or activities ofTrans-Activator of Transcription (Tat) or Transactivation Responsiveelements (TAR), molecules associated with Trans-Activator ofTranscription (Tat) or Transactivation Responsive element (TAR).

BACKGROUND

Although treatment with antiretroviral drugs (ARVs) has extended thequality and expectancy of life for people infected with humanimmunodeficiency virus (HIV), they have been unsuccessful in curing HIVinfection. Highly active antiretroviral therapy (HAART) is based ontriple or quadruple combinations of ARVs, however while reducing HIV tovery low levels, this treatment fails to eliminate the infectioncompletely (Clavel F. & Hance A. J. (2004) N Engl J Med 350, 1023-1035;Arhel N. & Kirchhoff F. (2010) Biochim Biophys Acta 1802, 313-321).Ultrasensitive assays revealed that HIV persists in latently andproductively infected CD4⁺T cells in the peripheral blood of individualsreceiving HAART who have maintained undetectable plasma viremia forprolonged periods of time (Chun T W, et al. (2005) J Clin Invest 115,3250-3255; Yukl S, et al. (2010) 17^(th) Conference on Retroviruses andOpportunistic Infections, San Francisco; Palmer S, et al. (2008) ProcNatl Acad Sci USA 105, 3879-3884). Residual viremia is not affected bythe addition of an integrase or a fusion inhibitor to a stable HAARTregimen, suggesting that it originates from long-lived stable reservoirsthat contain an integrated provirus that continuously produces viralparticles despite HAART. Since viral production from these cellularreservoirs results from the continuous transcription of an integratedviral genome, they are not affected by NRTI, NNRTI, PIs, INIs or FIs.

SUMMARY

This Summary is provided to present a summary of the invention tobriefly indicate the nature and substance of the invention. It issubmitted with the understanding that it will not be used to interpretor limit the scope or meaning of the claims.

Embodiments are directed to pharmaceutical compositions comprisinganti-Tat drugs and anti-Tat drug candidates.

In other preferred embodiments, methods of preventing a viral infectionor treating patients suffering from a viral infection, such as forexample, human immunodeficiency virus (HIV) are provided.

In one embodiment, a method of preventing viral infection or treating aviral infection in a patient, comprises administering to the patient atherapeutically effective amount of an inhibitor of retroviraltranscription wherein the inhibitor inhibits retroviral transcription ascompared to a control. In one embodiment, the retrovirus is a humanimmunodeficiency virus (HIV). In another embodiment, the retrovirus is ahuman T-cell leukemia virus (HTLV). However, any retrovirus iscontemplated.

In preferred embodiments, the inhibitor of retroviral transcriptioninhibits function or activity of a Trans-Activator of Transcription(Tat), a molecule associated with Trans-Activator of Transcription(Tat), a molecule associated with Transactivation Responsive element(TAR) a Transactivation Responsive element (TAR) and/or interactionbetween a Trans-Activator of Transcription (Tat) and a TransactivationResponsive element (TAR), DNA-PK or combinations thereof. Preferably,the inhibitor of retroviral transcription comprises: cortistatins,cortistatin derivatives, analogs, substituted cortistatins or saltsthereof. An example of a cortistatin is cortistatin A. An example of acortistatin analog is didehydro-Cortistatin A (dCA).

Other aspects are described infra.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1H show the structure and activity of dCA on HIV-1 expression.

FIG. 1A: Structure of Cortistatin A and of its analogdidehydro-Cortistatin A (dCA).

FIG. 1B: Activity of dCA on acute replication of HIV-1 at threedifferent MOIs. HeLa-CD4 cells were plated at 1×10⁴ cells per well of a96-well plate, and 24 h later the indicated dilutions of HIV-1 pNL4-3were added to the cells in the presence of dCA or DMSO. Forty-eighthours post infection a quantitative chlorophenolred-β-D-galactopyranoside (CPRG) assay was performed.

FIG. 1C: Effect of pre-treating cells with dCA on acute HIV-1replication. HeLa-CD4 cells were either treated or not with increasingconcentrations of dCA. Twenty-four hours later HIV-1 pNL4-3 was added tothe cells of both experiment sets (MOI>>10) in the presence of testingcompound or DMSO control. CPRG assay performed 48 h later.

FIG. 1D: dCA does not block HIV-1 proviral integration into host cells.HeLa-CD4 cells were infected with pNL4-3 (MOI>>1) in the presence ofdCA. Total DNA was extracted 24 hours later and integrated provirus wasdetermined by quantitative PCR (qPCR).

FIG. 1E: Analysis of viral mRNA expression. Total RNA was extractedthree days after acute infection with pNL43 (MOI>>1) in the presence ofdCA. First-strand cDNA was synthesized with random primers and targetDNA was quantified by qPCR using primers recognizing the env and LTRregions. Results were normalized as copies of viral mRNA per copy ofGAPDH mRNA. The arbitrary value of 1 was assigned to the amount of viralmRNA generated in the absence of dCA. RNA samples not reversetranscribed were used as negative control. Error bars represent standarddeviations.

FIG. 1F: Viral mRNA expression levels upon dCA treatment of chronicallyinfected cells. HeLa-CD4 cells chronically infected with pNL4-3 weretreated with dCA for 10 or 60 days, total RNA was extracted, reversetranscribed using random primers, and the quantification of viral cDNAwas performed as in FIG. 1E.

FIG. 1G: p24 antigen quantification. Viral supernatants recovered fromcells described in FIG. 1B, grown for 60 days, were assayed for theirp24 antigen content using a sandwich ELISA kit. Error bars representstandard deviations.

FIG. 1H: Viral RNA levels upon treatment of CEM SS cells with dCA andknown antiviral drugs. CEM SS cells chronically infected with pNL4-3were treated with the indicated compounds for 7 days. Quantification ofviral RNA was performed as in FIG. 1E.

FIGS. 2A-2G show that dCA binds to Tat and inhibits Tat transactivationof the HIV-1 LTR.

FIG. 2A: dCA prevents transactivation of the HIV-1 promoter byrecombinant Tat. HeLa-CD4-LTR-Luc cells were treated with 0.5 μMrecombinant Tat protein with increasing concentrations of dCA.Chloroquine 100 μM was added to increase Tat uptake was added to allpoints except untreated wells. Luciferase activity was measured 24 hlater using the Luciferase Assay System (Promega). Luciferase activityper protein concentration of each sample is shown as relative lightunits (RLU). HI: Heat Inactivated.

FIG. 2B: HeLa-LTR-Luc cells were transfected with 2 μg of a constructexpressing Tat-flag driven by the thymidine kinase (TK) promoter.Twenty-four hours later cells were split and treated or not with dCA atthe indicated concentrations. Forty hours later RLU determined as inFIG. 2A. RLU at 0 nM dCA set as 100% activation.

FIG. 2C: Schematic diagram of the HIV-1 Tat protein. Indicated are knowndomains involved in either transactivation or interaction with hostfactors. Depicted above is the amino acid sequence of the wild-typebasic domain or a mutated form that is deficient in binding to the TARloop.

FIG. 2D: Structure of biotinylated cortistatin A.

FIG. 2E: dCA binds to TAR but not to TAR non-binding mutant of Tat.HEK293T cells were transfected with flag-tagged Tat 101 a.a.(Tat-F-101-wt), a shorter Tat version with 86 a.a. (Tat-F-86-wt), Tat 86a.a. mutated in the basic domain (Tat-F-BRM), flag-tagged CDK11(CDK11-F), flag-tagged 9G8 (9G8-F) and empty vector control. Forty hourslater, protein extracts were incubated with DYNABEADS MYONE™Streptavidin T1 coated with either Biotin or Bio-dCA. Pulled-downproteins were revealed by Western blotting with the indicatedantibodies.

FIG. 2F: dCA interacts with purified recombinant Tat protein.Recombinant Tat protein was incubated with Bio-dCA streptavidin-coatedbeads in the presence or absence of an excess of non-biotinylated dCA(represented as molar equivalent [eq.] of Bio-dCA). Raltegravir andrecombinant GST-9G8 were used as a negative control competitor or asnegative protein-binding control, respectively. Pulled-down proteinswere revealed by Western blot with anti-Tat and anti-GST antibodies.

FIG. 2G: dCA alters Tat-Flag cellular localization. Confocal microscopyanalysis of the sub-cellular localization of transfected Tat-F-86-F andTat-F-86-BRM and where indicated treated (24 h) or not with dCA. Flagepitope-tagged Tat was recognized with anti-flag and AlexaFluor 568anti-IgG. Transfections were performed in HeLa-CD4 cells. Magnification300×.

FIGS. 3A-3C: RNAPII elongation from viral promoter is inhibited by dCA.

FIG. 3A: Schematic representation of the HIV genome and localization ofprimers.

FIG. 3B: HIV-1 elongation from HIV-1 promoter measured by qPCR. Leftpanel: Total RNA was recovered from chronically infected HeLa cellstreated with increasing amounts of dCA for 60 days, reverse transcribedusing random primers and viral cDNA was measured by relative qRT-PCRusing the indicated primers located either at 100 bp, 5.3 kb or 8.5 kbdownstream from the transcript start site. All messages were normalizedrelative to GAPDH mRNA. The 100% value was arbitrarily assigned to theamounts of viral mRNA generated in the absence of compound, measured at100 by from start site. Right panel: Plotting of data obtained in leftpanel, setting each data point obtained with the 100 by primer set at100% and comparing to results obtained with 5.3 kb primer set.

FIG. 3C: ChIP assay of the HIV promoter. HeLa-CD4 cells chronicallyinfected with pNL4-3 were treated with dCA for 4 days and flavopiridol(Flay) for 6 h followed by protein-DNA crosslinking. Lysates weresonicated, the crosslinks were reversed and RNAPII wasimmunoprecipitated. DNA was measured by qPCR using the indicated set ofprimers. ChIP values are represented as percentages of input. Errorbars, ±s.d. (n=3). *P<0.05; **P<0.01 (unpaired t-test).

FIGS. 4A-4B: No viral rebound upon termination of dCA treatment.

FIG. 4A: HeLa-CD4-LTR-LacZ cells chronically infected with pNL43 weretreated with dCA for 60 days and treated with dCA for another 10 days(dCA) or stopped dCA treatment for 10 days (dCA Stop). Total RNA wasextracted and reverse transcribed with random hexamer primers. The viralmRNA copies were quantified by qPCR and normalized with GAPDH mRNA.Viral mRNA output from untreated cells was assigned as 1. RNA extractswere used in the qPCR as negative control for the presence of genomicDNA contamination, 0.1% of the amplification of the cDNA samples is dueto genomic DNA. The error represents a covariance of less than 5%.

FIG. 4B: Same as in FIG. 4A however the treatment was stopped for 27days before harvest of the cells.

FIGS. 5A-5I: Potency of dCA and activity of dCA in primary cells.

FIGS. 5A-5D: Effect of dCA on acute replication of HIV-1 compared withknown retroviral inhibitors. HeLa-CD4 cells were infected with HIV-1pNL4-3 in the presence of the indicated compounds or DMSO. Forty hourspost infection a CPRG assay was performed. Same dCA curve plotted ingraphs FIGS. 5A-5D. Error bars represent standard deviation.

FIG. 5E: Analysis of viral mRNA expression upon treatment with dCA andretroviral inhibitors. Total RNA extracted four days after acuteinfection with pNL4-3 (MOI>>1) in the presence of drugs. First-strandcDNA was synthesized with random primers, and quantified by qPCR usingprimers recognizing the env and LTR regions. Results were normalized ascopies of viral mRNA per copy of GAPDH mRNA. The arbitrary value of 1was assigned to the DMSO control. RNA samples that were not reversetranscribed were used as negative control. Error bars represent standarddeviation.

FIG. 5F: Activity of dCA on acute HIV-2 replication. HeLa-CD4 cellsinfected with ROD/A in the presence of the indicated concentrations ofdCA. Antigen p24 in the supernatant measured using a sandwiched ELISAkit, 5 days post-infection.

FIG. 5G: Activity of dCA on chronic HIV-2 replication. HeLa-CD4 cellschronically infected with ROD/A in the presence of the indicatedconcentrations of dCA. Antigen p24 in the supernatant measured as inFIG. 5F, 7 days post-infection.

FIGS. 5H-5I: Activity of dCA on primary cells. Freshly isolateduninfected human PBMCs were stimulated with PHA for two days, washed,and grown from then on in IL-2 alone. Cells were infected with pNL43 inthe presence of increasing concentrations of dCA and raltegravir.Antigen p24 was measured 5 days post infection using a sandwich ELISAkit.

FIGS. 6A-6B: dCA activity on CD4⁺T cells from viremic and aviremicHIV-infected subjects.

FIG. 6A: dCA effect on CD4⁺T cells isolated from viremic subjects. Viralproduction from CD4⁺T cells isolated from five viremic subjects andgrown in IL-2 was measured in the presence or absence of ARVs(RAL+AZT+EFV) supplemented or not with 100 nM dCA. Viral production wasmeasured in the supernatant by a sensitive in-house ELISA for capsid p24and normalized to the negative control (Mock). Statistical significancewas assessed by a paired t-test.

FIG. 6B: dCA effect on CD4⁺T cells isolated from aviremic subjects.CD4⁺T cells isolated from PBMCs from four subjects who had been treatedwith HAART for at least 3 years were cultured for 6 days without IL-2 inthe presence of ARVs to block de novo infection. dCA (100 nM) effect onthe spontaneous release of HIV particles was assessed by measuring viralRNA in culture supernatants by ultrasensitive RT-PCR.

FIG. 7 shows the effect of dCA on cell viability. Mitochondrialmetabolic activity. MTT(3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay onHeLa-CD4 cells incubated with increasing concentrations of dCA for 4days.

FIGS. 8A-8D show the transcriptional activity of the CXCR4, TK and CD4promoters or NFκB reporter plasmid, not affected by dCA.

FIG. 8A: HeLa-CD4-LTR-Luciferase cells were treated with dCA and/or PMAat 10 nM for 8 hours. Luciferase activity measured and results adjustedper protein concentration of each sample, relative light units (RLU).

FIG. 8B: TE671 cells were transfected with an NF-kB luciferase reporterplasmid. The following day cells were treated with TNF-α in presence orabsence of dCA. Cells were lysed 5 hours later and Luciferase activitywas measured as in FIG. 8A.

FIG. 8C: Luciferase assays of TE671 cells transfected with the indicatedpromoter or promoter portion driving Luciferase expression. Mainconsensus bonding sites for transcription factors are indicated. 24 hpost transfection cells were split and treated or not with CA. Fortyhours later cells were lysed and luciferase activity measured as in FIG.8A.

FIG. 8D: CEM SS and HeLa-CD4 cells stained for CD4, CXCR4 or isotypecontrol expression followed by flow cytometry analysis.

FIGS. 9A-9B: Biotinylated dCA activity and cell viability.

FIG. 9A: Activity of Bio-dCA and dCA on acute HIV-1 infection,HeLa-CD4-LTR-LacZ cells reporter assay.

FIG. 9B: Mitochondrial Metabolic activity of HeLa-CD4 cells in thepresence of Bio-dCA.

FIGS. 10A-10B: dCA does not inhibit CDK11 activity in vitro.

FIG. 10A: Kinase activity of CDK11 tested in vitro with 9G8 as substratein presence of dCA (0.1 to 10 μM) or DMSO equivalent. CDK11 DN is akinase inactive mutant used as negative control.

FIG. 10B: Expression of endogenous CDK11 in TE671 cells was notdisturbed by increasing concentrations of dCA treatment for 48 h.Western blot with the indicated antibodies.

FIGS. 11A-11D: Effect of dCA on Tat-Flag cellular localization. Confocalmicroscopy analysis of the sub-cellular localization of transfected wtTat(101)-1-flag, Tat(86)-1-BRM-flag, Tat-2-flag, Δ2-26-Tat(101)-1-flagand where indicated treated (24 h) or not with dCA. Flag recognized withanti-flag and AlexaFluor 568 anti-IgG antibodies. Endogenous fibrillarinstained with anti-fibrillarin and FITC-anti-IgG antibodies.

FIG. 11A: dCA dose response to Tat-flag and fibrillarin-GFPlocalization.

FIG. 11B: Effect of dCA on Tat or variants and fibrillarin.

FIG. 11C: No effect of dCA on cyclin T1. Endogenous cyclinT1 stainedwith anti-CyclinT1 and FITC-anti-IgG antibodies.

FIG. 11D: Bio-dCA affects Tat sub-cellular localization. AllTransfections performed in HeLa cells. Magnification 300×.

FIG. 12: ChIP assay of the GAPDH promoter and ORF. HeLa-CD4 cellschronically infected with pNL4-3 were treated with dCA for 4 days andFlavopiridol (Flav) for 6 h followed by protein-DNA crosslinking.Lysates were sonicated, the crosslinks were reversed and RNAPII wasimmunoprecipitated. DNA was measured by qPCR using primers specific forGAPDH promoter or ORF regions. ChIP values are represented aspercentages of input. Error bars, ±s.d. (n=3).

FIGS. 13A-13B: Effect of dCA on cell viability.

FIG. 13A: Mitochondrial metabolic activity. MTT(3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay onuninfected stimulated PBMCs incubated with increasing concentrations ofdCA for 4 days.

FIG. 13B: Uninfected PBMCs staining with violet fluorescenceamine-reactive viability dye (ViViD) or Annexin V. ViViD-AnnexinV-cellsrepresent viable cells in the presence of increasing concentrations ofdCA upon incubation with dCA for 1 or 3 days.

FIG. 14: Bio-CA associated proteins. Pull down assay using DYNABEADS®MYONE™ Streptavidin T1 coated with either biotin (CTRL) or Bio-CA fromP42 cellular protein extract infected or not with pNL4-3 and treated ornot with 1 μM CA 48 h. After SDS-PAGE analysis and Coomassie staining,gel slices were trypsin-digested and sent to mass spectrometry analysis.

FIG. 15: CA binds Tat but not to TAR-nonbinding mutant of Tat. HEK293Tcells were transfected with wt-Tat101-flag, wtTat86-flag,Tat86mutant-TAR domain, CDK11-flag or 9G8-flag as negative control.Forty hours later, protein extracts were incubated with DYNABEADS®MYONE™ Streptavidin T1 coated with either biotin or Biotinylated-CA.Pulled down proteins analyzed by Western blot with the indicatedantibodies.

DETAILED DESCRIPTION

HIV drug therapy is based on the administration of drugs incombinations, in order to minimize development of mutations that canconfer single-drug resistance to the virus. For optimal efficacy, drugsshould target different stages of the virus life cycle. The viralprotein Tat, a potent activator of HIV gene expression, is a potentialantiviral target. Tat is required for viral gene expression during theexponential growth of the virus, as well as for transcription of theintegrated proviral genome that gives rise to the mutation-rich genomicRNA from which drug-resistant strains of HIV-1 emerge. Because Tat iscrucial for virus replication, it is the target for the development of,several active compounds; however these showed low efficacy and none hasyet been reported to have completed clinical trials.

Several aspects of the invention are described below with reference toexample applications for illustration. It should be understood thatnumerous specific details, relationships, and methods are set forth toprovide a full understanding of the invention. One having ordinary skillin the relevant art, however, will readily recognize that the inventioncan be practiced without one or more of the specific details or withother methods. The present invention is not limited by the illustratedordering of acts or events, as some acts may occur in different ordersand/or concurrently with other acts or events. Furthermore, not allillustrated acts or events are required to implement a methodology inaccordance with the present invention.

Definitions

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. Furthermore, to the extent that the terms “including”,“includes”, “having”, “has”, “with”, or variants thereof are used ineither the detailed description and/or the claims, such terms areintended to be inclusive in a manner similar to the term “comprising.”

The term “about” or “approximately” means within an acceptable errorrange for the particular value as determined by one of ordinary skill inthe art, which will depend in part on how the value is measured ordetermined, i.e., the limitations of the measurement system. Forexample, “about” can mean within 1 or more than 1 standard deviation,per the practice in the art. Alternatively, “about” can mean a range ofup to 20%, preferably up to 10%, more preferably up to 5%, and morepreferably still up to 1% of a given value. Alternatively, particularlywith respect to biological systems or processes, the term can meanwithin an order of magnitude, preferably within 5-fold, and morepreferably within 2-fold, of a value. Where particular values aredescribed in the application and claims, unless otherwise stated theterm “about” meaning within an acceptable error range for the particularvalue should be assumed.

“Treating” or “treatment” of a state, disorder or condition includes:(1) Preventing or delaying the appearance of clinical or sub-clinicalsymptoms of the state, disorder or condition developing in a mammal thatmay be afflicted with or predisposed to the state, disorder or conditionbut does not yet experience or display clinical or subclinical symptomsof the state, disorder or condition; or (2) Inhibiting the state,disorder or condition, i.e., arresting, reducing or delaying thedevelopment of the disease or a relapse thereof (in case of maintenancetreatment) or at least one clinical or sub-clinical symptom thereof; or(3) Relieving the disease, i.e., causing regression of the state,disorder or condition or at least one of its clinical or sub-clinicalsymptoms. The benefit to a subject to be treated is either statisticallysignificant or at least perceptible to the patient or to the physician.Thus, “treating a retroviral infection”, for exampl,e HIV should beunderstood as treating a patient who is at any one of the several stagesof HIV infection progression, which, for example, include acute primaryinfection syndrome (which can be asymptomatic or associated with aninfluenza-like illness with fevers, malaise, diarrhea and neurologicsymptoms such as headache), asymptomatic infection (which is the longlatent period with a gradual decline in the number of circulating CD4⁺ Tcells), and AIDS (which is defined by more serious AIDS-definingillnesses and/or a decline in the circulating CD4 cell count to below alevel that is compatible with effective immune function).

“Patient” or “subject” refers to mammals and includes human andveterinary subjects. The terms include any organism at risk of having oractually having a retroviral infection such as, for example, HIV, SIV,or SHIV, such as an mammal, including a macaque or human.

The term “HIV infection” generally encompasses infection of a host,particularly a human host, by the HIV family of retroviruses including,but not limited to, HIV I (also known as HTLV-III, LAV-1, LAV-2), andHIV II and the like. “HIV” can be used herein to refer to any strains,forms, subtypes, clades and variations in the HIV family. Thus, treatingHIV infection will encompass the treatment of a person who is a carrierof any of the HIV family of retroviruses or a person who is diagnosed ofactive AIDS, as well as the treatment or prophylaxis of the AIDS-relatedconditions in such persons.

The term “SHIV” generally refers to a number of chimeric virusesconstructed by recombinant DNA technology from parental viruses, simianimmunodeficiency virus (“SIV”) and HIV.

The term “preventing” refers to a process by which an initial HIVinfection is prophylactically obstructed or the progression of which isinhibited or delayed. The term “preventing HIV infection” may alsoencompass treating a person who has not been diagnosed as having HIVinfection but is believed to be at risk of infection by HIV.

A “prophylactically effective amount” refers to an amount effective, atdosages and for periods of time necessary, to achieve the desiredprophylactic result. Typically, since a prophylactic dose is used insubjects prior to or at an earlier stage of disease, theprophylactically effective amount will be less than the therapeuticallyeffective amount.

As used herein, the terms “cortistatin(s)”, “cortistatin agents” ,“cortistatin molecules” are used interchangeably herein and the termsare meant to include any cortistatin, cortistatin derivatives, analogs,substituted cortistatins or salts thereof. See, also for example,compounds having structures corresponding to Formulae I through XIII.

As used herein, “function” of a certain molecule (e.g. Tat, TAR) refersto any function that the molecule performs. Modulation of the function(e.g. binding to a molecule, transcription, translation, etc) ismeasured in the presence or absence of cortistatin agents as compared tocontrols.

As used herein, “activity” of a certain molecule refers to expression ofor efficiency or degree to which that specific function is performed bythe molecule in the presence or absence of the cortistatin agent ascompared to a control. For example, if the function of the molecule istranscription, then the transcriptional activity can be measured. See,for example, the examples section which follow.

As used herein, the term “associated with” refers to any interactionsone molecule may have with another either directly (e.g. binding to,enzymatic activity, etc.) or indirectly (e.g. modulates another moleculewhich has an effect on a different molecule (e.g. biochemical pathways,transcription pathways, enzymatic pathways, signaling etc.).

“Detectable moiety” or a “label” refers to a composition detectable byspectroscopic, photochemical, biochemical, immunochemical, or chemicalmeans. For example, useful labels include ³²P, ³⁵S, fluorescent dyes,electron-dense reagents, enzymes (e.g., as commonly used in an ELISA),biotin-streptavidin, dioxigenin, haptens and proteins for which antiseraor monoclonal antibodies are available, or nucleic acid molecules with asequence complementary to a target. The detectable moiety oftengenerates a measurable signal, such as a radioactive, chromogenic, orfluorescent signal, that can be used to quantify the amount of bounddetectable moiety in a sample. Quantitation of the signal is achievedby, e.g., scintillation counting, densitometry, or flow cytometry.

Anti-Viral Agents

Although treatment with antiretroviral drugs has dramatically benefittedHIV-infected individuals, it has had a negligible impact on the globalAIDS epidemic. AZT (zidovudine), introduced 25 years ago, was the firstof approximately 30 antiretroviral drugs that have been licensed and arenow in clinical use. Antiretroviral drugs fall in the following majorclasses: Fusion inhibitors (FIs), nucleoside reverse transcriptaseinhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors(NNRTIs), nucleotide reverse transcriptase inhibitors (NtRTIs), proteaseinhibitors (PIs) and integrase inhibitors (INIs). Highly activeantiretroviral therapy (HAART) is based on triple or quadruplecombinations of NRTIs, NNRTIs and PIs and while reducing HIV to very lowlevels, fails to eliminate the infection completely and ultimately leadsto the emergence of drug-resistant mutant strains. Thus, it is highlydesirable to develop new anti-HIV agents with superior efficacy andsafety profiles. Identification of compounds that repress HIVtranscription activation is important, not only because it wouldconstitute a new class of antiretroviral drugs, but also, due to thenature of their mode of action they could drastically reduce theemergence of drug-resistant strains.

In a preferred embodiment, an anti-viral agent comprises cortistatins,cortistatin derivatives, analogs, substituted cortistatins or saltsthereof. An example of a cortistatin analog is a didehydro-cortistatin A(dCA). Cortistatins constitute a family of eleven steroidal alkaloids,isolated from the marine sponge Corticium simplex. The results obtainedand described in the examples section which follows, evidence thatcortistatin A is a promising anti-Tat drug candidate. Briefly, it wasfound that didehydro-cortistatin A (dCA) was a very potent inhibitor ofTat-activated transcription of the HIV-1 provirus. dCA was extremelyefficient at reducing viral output from acutely infected cells, as wellas from chronically infected cultured cells or freshly isolatedperipheral blood lymphocytes (PBLs). The EC₅₀ of dCA for abrogatingchronic HIV infection was less than 0.1 nM, a value >10 times lower thanthat for AZT (zidovudine; 5.2 nM), an antiviral currently usedclinically. The cytotoxic concentration (CC₅₀) for dCA in cultured celllines or freshly isolated PBLs was 20 μM, which confers on dCA atherapeutic index of approximately 200 000. Using biotinylated dCA, itwas further demonstrated that dCA interacted directly with Tat, but notwith a mutant version of Tat that fails to bind to its viral RNA target,TAR. Also identified was the interaction between dCA and theDNA-dependent protein kinase (DNA-PK) catalytic subunit by massspectrometry in both infected and uninfected cells. Upon HIV infectionDNA-PK tightly associates with Tat to promote the phosphorylation of thetranscription factor Sp1, which results in increased HIV-1 transcriptioninitiation, via three Sp1 binding sites in the core of the HIV-1promoter. Without wishing to be bound by theory, it was hypothesizedthat dCA represses HIV replication in two ways; on the one handinhibiting Tat-TAR interaction, and consequently inhibiting elongationby RNA Polymerase II (Pol II) from the HIV promoter; and on the otherinhibiting DNA-PK activation of Sp1, and initiation of transcription byPol II. Both routes would result in repression of HIV-1 transcriptionalactivation. DNA-PK is an example of one molecule which is associatedwith Tat.

Treatment of the viral infected cells in the viral infection withcortistatin molecules or agents results in inhibition of viralreplication. Inhibition of viral replication with the method of thepresent invention results in suppression or a slowing down of thedevelopment of the disease and the elimination of the virus due to itsinability to replicate, for example. Treatment can also provide adecrease of any symptoms of the viral infection that are present. Themethods of the present invention are particularly useful in treatingpatients suffering from HIV infection to prevent the development of fullblown AIDS. The methods of the present invention are also useful fortreating a patient having AIDS. The methods of the present invention areparticularly useful for treating patients having both an HIV infectionand any associated disorders.

Retroviral replication: A determinant step in the replication of allretroviruses, including HIV-1, is the reverse transcription of the viralgenomic RNA into cDNA and integration of the proviral genome into thehost chromosome. The HIV-1 5′ Long Terminal Repeat (5′LTR) becomes aneukaryotic transcription unit and transcription is then regulated by aninterplay between a combination of viral and cellular transcriptionfactors with binding sites present in the LTR. The LTR contains twotandem NF-kB elements followed by three tandem Sp1 binding sites and theTATA box sequence. NF-kB sites are required for basal transcription andSp1 binding sites and the TATA box are required for basal transcriptionand Tat-mediated transactivation. After integration, RNA Polymerase II(Pol II) is recruited to the 5′LTR promoter and the viral genome istranscribed back into RNA. During the early phases of transcription,when the HIV transactivator Tat has not been yet made, cellular Pol IIassembles at the promoter, and is initially phosphorylated at theC-terminal domain (CTD) by CDK7 kinase, which is part of the generaltranscription factor TFIIH. The modified Pol II clears the promoter andstarts transcription of TAR, but Pol II stalls right after initiationand is inefficiently converted into the processive form. Only short nonpolyadenylated transcripts are produced (+1 to +59). Eventually Pol IIis able to transcribe the entire proviral genome and the transcript isspliced producing an mRNA that encodes the viral Tat protein. Efficientelongation requires the recruitment by Tat of the positive transcriptionelongation factor b (P-TEFb) to a promoter proximal element (TAR), anRNA stem loop structure that spontaneously forms at the 5′ extremitiesof the viral pre-mRNA. P-TEFb is composed of cyclin T1 and of cyclindependent kinase 9 (CDK9), and is used at many promoters, includingHIV-1, to phosphorylate serine 2 residues of the Pol II CTD, convertinga nonphosphorylated form (Pol IIa) to a hyperphosphorylated form (PolIIo) that engages in productive elongation. It has recently been foundthat Tat assembles first with P-TEFb before binding to TAR. The HIV-2LTR is organized similarly to HIV-1 LTR and it contains a TAR elementlocated downstream of the transcriptional initiation start site. Unlikethe HIV-1 TAR element, which contains a single stem-loop, the HIV-2 TARelement consists of 2 characteristic stem-loop structures, both of whichparticipate in optimal Tat response. While the HIV-1 TAR responds toHIV-1 and HIV-2 Tat equally well, the HIV-2 TAR element responds toHIV-2 tat somewhat more efficiently than to HIV-1 tat.

Tat protein contains 101 residues, with 1-72 amino acids encoded by afirst exon and residues 73-101 encoded by a second exon, is consideredas containing several domains. It should be noted that whereas an 86amino acid form of Tat, which exists for a few laboratory-passaged virusstrains (e.g. LAI, HXB2, pNL43), has been frequently used, this versionrepresents a truncated and not naturally occurring full-length protein.In fact, a single nucleotide change in LAI, XB2 and/or pNL43 at putativeresidues 87 unmasks the conserved 101 amino acid protein.

When the provirus is integrated into the host chromosome it is packagedinto chromatin and the LTR activity in the absence of any stimuli issilent. Tat-associated histone deacetylases TAHs (which include p300/CBPand p300/CBP-associating factor, PCAF) induce activation ofchromatinized HIV-1 LTRs presumably through acetylation of histones.TAHs also directly acetylate Tat protein, regulating itsassociation/dissociation to TAR that allow for Tat to bind to nascentTARs and to other cellular factors.

Tat also facilitates enhanced transcriptional initiation. Tat activationmay be facilitated through protein-protein interactions with thetranscription factor Sp1. Sp1 factors binding to the GC rich region ofthe HIV LTR may facilitate Tat recruitment proximal to the basaltranscription machinery. Sp1 serves basal and activated functions at theHIV-1 promoter. In the absence of Tat, the HIV-1 LTR has a cleardependence on Sp1 for basal expression. At a later stage of virusreplication, Sp1 cooperates synergistically with Tat to enhance furthertranscription from the LTR. Sp1 has been shown to interact with theTATA-binding protein (TBP), TBP tightly associated factor TAF110. TBPand TAF110 may function as coactivators that are essential foractivated, but not basal, transcription. Additionally, mutationalanalysis of Sp1 and NF-kB binding sites may indicate functionalcooperation between these two molecules. Sp1 is post-transcriptionallymodified by glycosylation and phosphorylation in a manner thatcorrelates with function. Double stranded DNA-dependent protein kinase(DNA-PK) has been identified as an SP1 kinase. DNA-PK is aserine/threonine multiprotein kinase comprised of a 350-kD catalyticsubunit, p350, and Ku subunits (p70 and p80), which bind to nucleicacids. DNA-PK plays a role in DNA double strand break repair and inmediating V(D)J recombination events. Tat has been shown to interactdirectly with Sp1 and DNA-PK and this interaction seems to promote Sp1phosphorylation, which consequently increases transcription from the HIVLTR.

In a preferred embodiment, an agent, such as for example, dCA inhibitsHIV replication. The inhibition of replication could be due to anynumber of mechanisms, including, for example, inhibition oftranscription initiation and/or elongation and/or possible dCAinhibition of Tat-TAR interaction in vivo. The various mechanism(s) ofaction include whether CA or dCA affect initiation of RNPII from theviral promoter and/or the elongation stimulated by Tat. The 5′ terminalregion (+1 to +59) of all HIV mRNAs forms an identical stem-bulge-loopstructure called the Transactivation Responsive (TAR) element. Tat bindsto TAR and activates transcription from the HIV LTR promoter. Basaltranscription from the integrated HIV LTR is very low and Tat and hostfactors increase the mRNA production from the integrated viral genome upto 100 fold. Mutations in the TAR sequence usually affect Tat functionand HIV replication, indicating a strong requirement for conservation ofthis structure. Without wishing to be bound by theory, it ishypothesized that TAR is a potential therapeutic target and anti-Tatdrugs would have a synergistic effect with other inhibitors.

Screening based on Tat-TAR interaction has identified a number ofcompounds, however further characterization demonstrated these were onlyinhibitors of viral entry. Other molecules such as trans-dominant Tatmutants, TAR RNA analogs, antisense oligonucleotides, ribozymes, andpolypeptides have all been used to inhibit the interaction between Tatand TAR or Tat and other cellular co-activators; but none of them iscurrently used in therapeutics partly because some of these strategiesmay not easily be delivered for an efficient therapy, emphasizing theneed for small molecule compounds.

In the examples section which follows, the pharmacokinetics datademonstrated that CA and dCA could be dosed intraperitoneally or orallyand plasma drug levels after 24 h post dose were still above the EC₅₀value found in cell-based assays. The data shown herein, CA EC₅₀ for theinhibition of HIV activity is in the picomolar to low nanomolar rangewhile CC₅₀ is 20 μM, conferring to CA an extremely high therapeuticindex. CA specifically binds to Tat and this molecular interaction isprobably at the basis of the inhibition of the TAR-mediatedtransactivation of the viral promoter. The data herein also show that CAand/or dCA binds DNA-dependent protein kinase. This interaction mayresult in reduced phosphorylation of Sp1, which might translate into areduction of the basal activity of the promoter. Both events lead to anextremely efficient reduction of HIV viral transcription that in turnlimits drastically the emergence of drug resistant mutants, rendering CAand/or dCA a very exciting and attractive anti-HIV compound.

In another preferred embodiment, a method of preventing viral infectionor treating a viral infection in a patient, comprises administering tothe patient a therapeutically effective amount of a cortistatin,including, for example, analogs, substituted cortistatin molecules,derivatives and the like. Preferably, the viral infection is a humanimmunodeficiency virus (HIV) infection. In some embodiments, thecortistatins can be administered with one or more pharmaceuticals usedin treating HIV-infected patients. In a preferred embodiment, thecortistatin is cortistatin A and/or dCA. The administration of thecortistatin agents can be part of an antiviral therapy or can beadministered alone. For example, HIV infected patients who areundergoing HAART therapy protocols can have any of the cortistatinagents administered pre-HAART, in conjunction with or after HAARTtherapy. In some embodiments, the doses and times of administration canbe modified to tailor the therapy depending on the patient's condition,e.g. viral load, age, years of infection, weight, sex, and the like.

The antiviral drugs comprise one more of: fusion inhibitors (FIs),nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleosidereverse transcriptase inhibitors (NNRTIs), nucleotide reversetranscriptase inhibitors (NtRTIs), protease inhibitors (PIs) orintegrase inhibitors (INIs).

In another preferred embodiment, a method of modulating retroviralreplication in vitro or in vivo comprises administering to a cell orpatient an effective amount of cortistatin A and/or dCA. Preferably, theretroviral replication is modulated by at least 20% as compared to abaseline control, more preferably, the retroviral replication ismodulated by about 90%, 95%, 96%, 97%, 98%, 99% or 100% as compared to abaseline control.

The inhibition or retroviral replication can be measured by any meansknown in the art e.g. pfu. Inhibitors of retroviral transcription can bemeasured by any methods known in the art. Exemplary methods aredescribed in the examples section which follows. Modulators of Tat-TARinteractions, modulators of Tat or TAR functions or activities andidentification of any molecules associated with these can be measured byany number of assays, e.g. pull-down assays, immunoassays, and the like.See, examples section which follows.

In another preferred embodiment, a method of inhibiting interaction ofhuman immunodeficiency virus Trans-Activator of Transcription(Tat)-Transactivation Responsive element (TAR) in a cell or patient,comprises administering to the cell or patient an effective amount ofcortistatin A and/or dCA. Preferably, the cortistatin agent inhibitsretroviral transcription by modulating the function or activity of aTrans-Activator of Transcription (Tat), a Transactivation Responsiveelement (TAR), a molecule associated with Trans-Activator ofTranscription (Tat) (e.g. binds to Tat or modulates the function oractivity of Tat), a molecule associated with Transactivation Responsiveelement (TAR) (e.g. binds to TAR or modulates the function or activityof TAR), and/or interaction between a Trans-Activator of Transcription(Tat) and a Transactivation Responsive element (TAR) in patients.

In another preferred embodiment, a method of modulating function oractivity of a human immunodeficiency virus (HIV) transcriptionalpromoter in vitro or in vivo comprises administering a therapeuticallyeffective amount of an agent which modulates function or activity of aTrans-Activator of Transcription (Tat), a Transactivation Responsiveelement (TAR), a molecule associated with Trans-Activator ofTranscription (Tat) (e.g. binds to Tat or modulates the function oractivity of Tat), a molecule associated with Transactivation Responsiveelement (TAR) (e.g. binds to TAR or modulates the function or activityof TAR), and/or interaction between a Trans-Activator of Transcription(Tat) and a Transactivation Responsive element (TAR). An example of amolecule t binds to Tat is DNA-PK. Preferably the agent is a cortistatinagent comprising: a cortistatin, cortistatin derivatives, analogs,substituted cortistatins or salts thereof.

In another embodiment, the cortistatin agent modulates HTLV replication.The HTLV Tax protein has some features which resemble HIV Tat. In oneembodiment, the cortistatin agent modulates activities, moleculesassociated with Tax or functions of Tax.

In another preferred embodiment, the cortistatin agent or moleculereduces or inhibits neurotoxicity. Tat released from infected lymphoidcells causes neuronal dysfunction associated with HIV-1 associatedneurocognitive disease (HAND) in 50-70% of infected individuals, despitecontrol of HIV replication in the periphery. CA binds within theneurotoxic domain of Tat (amino acids 31-61) and thereby reduce HAND.

In one embodiment, a method of preventing or treating neurotoxicity in apatient infected with a retrovirus, comprises administering to thepatient a therapeutically effective amount of an agent which modulatesfunction or activity of a Trans-Activator of Transcription (Tat), amolecule associated with Trans-Activator of Transcription (Tat), amolecule associated with Transactivation Responsive element (TAR) aTransactivation Responsive element (TAR) and/or interaction between aTrans-Activator of Transcription (Tat) and a Transactivation Responsiveelement (TAR), or DNA-PK.

Candidate Retroviral Inhibitors

Natural products have always been a valuable resource for thepharmaceutical industry, and many drugs derived from natural productshave been of great benefit in virtually all clinical therapeutic areas.The Kobayashi group (S. Aoki et al., J Am Chem Soc 128, 3148 (Mar. 15,2006)) isolated CA a novel steroidal alkaloid from the marine spongeCorticium simplex, which exhibits anti-angiogenic properties againsthuman umbilical vein endothelial cells (HUVECs). The scarce naturalsupply prompted the chemical synthesis of CA. The Baran's laboratoryroute to CA synthesis departs from the cheap and abundant steroid,prednisone and requires only 13 chemical steps to the synthesis ofdidehydro-CA, the equipotent analog of CA (J. Shi et al., Angew Chem IntEd Engl 48, 4328 (2009)). This synthesis approach is the only knownroute that can provide large (>gram) quantities of material in acost-effective manner.

The data, shown in the examples section which follows, evidences thatcortistatin A, a steroid drug like molecule, is a novel inhibitor of Tattranscriptional activation of HIV. No natural compounds have ever beenpreviously shown to inhibit HIV replication in human test subjects.Briefly, the preliminary pharmacokinetics data demonstrated that CAcould be dosed intraperitoneally or orally and plasma drug levels after24 h post dose were still above the EC₅₀ value found in cell-basedassays. CA EC₅₀ for the inhibition of HIV activity is in the picomolarto low nanomolar range while CC₅₀ is higher than 20 μM, conferring to CAan extremely high therapeutic index. CA specifically binds to Tat andthis molecular interaction is probably at the basis of the inhibition ofthe TAR-mediated transactivation of the viral promoter. The data alsoshow that CA binds DNA-dependent protein kinase. This interaction mayresult in a reduction of the accrued phosphorylation of Sp1 mediated byTat and of Tat itself, which might translate into a reduction of thebasal activity of the promoter. Both events lead to an extremelyefficient reduction of HIV viral transcription that in turn limitsdrastically the emergence of drug resistant mutants, rendering CA andany derivative, analog, and substituted CA molecule, a very exciting andattractive anti-HIV compound. In a preferred embodiment, apharmaceutical composition comprises cortistatin, cortistatinderivatives, analogs, substituted cortistatins or salts thereof. Thecortistatin is preferably cortistatin A. An example of a cortistatinanalog is a didehydro-cortistatin A (CA or dCA).

Candidate agents, such as for example, cortistatin derivatives, analogs,substituted cortistatins or salts thereof can be screened to determinewhether they would be effective therapeutic agents. The candidate agentsare not limited to cortistatins, but can be any type of molecule whichmay inhibit retroviral replication, such as, for example, HIV-1.

In some embodiments, the agents comprise aryl substituted compounds.See, for example, Shenvi et al., WO 2009/137335 incorporated herein byreference in its entirety).

In an embodiment, a cortistatin agent comprises a compound having ageneral structure of Formula I:

Wherein

W is the residuum of a saturated or unsaturated diol of 2 to about 12carbon atoms that has been reacted with a ketone group to form thedepicted ketal;

R² is COR, CO₂R, SO₂R, or P(O) (OR)₂, where R is hydrido (H), a straightchain, branched chain or cyclic alkyl, alkenyl, or alkynyl moiety, anaromatic, heterocyclic or alicyclic moiety that contains 1 to about 24carbon atoms, in which a heterocyclic moiety contains 1 to four ringsthat each contain up to four ring atoms other than carbon that can beoxygen, nitrogen or sulfur; and

R¹ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur.

In one embodiment, a compound of Formula I comprises a structurecorresponding to Formula II when W comprises 2 carbon atoms:

In another preferred embodiment, a cortistatin agent comprises acompound having a general structure of Formula VII:

Wherein:

W is the residuum of a saturated or unsaturated diol of 2 to about 12carbon atoms that has been reacted with a ketone group to form thedepicted ketal;

R² is COR, CO₂R, SO₂R, or P(O) (OR)₂, where

R is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains 1 to about 24 carbon atoms, in which a heterocyclicmoiety contains 1 to four rings that each contain up to four ring atomsother than carbon that can be oxygen, nitrogen or sulfur;

R¹ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; and

R³ is a removable C1-C21 hydroxyl protecting group.

In another preferred embodiment, a cortistatin agent comprises acompound having a general structure corresponding to Formula VIII:

Wherein:

W is the residuum of a saturated or unsaturated diol of 2 to about 12carbon atoms that has been reacted with a ketone group to form thedepicted ketal;

R¹ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur, —R⁴ is an acyl group COR, CO₂R, SO₂R, or P(O) (OR)₂ thatcontains 1 to about 24 carbon atoms that can be a C1-C24 straight chain,branched chain or cyclic alkyl, alkenyl, or alkynyl moiety, an aromatic,heterocyclic or alicyclic moiety, in which a heterocyclic moiety cancontain 1 to four rings that each contain up to four ring atoms otherthan carbon that can be oxygen, nitrogen or sulfur; and

R⁵ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms in which theheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur.

In one embodiment, a cortistatin agent of Formula VIII comprises acompound having a structure corresponding to Formula III when W contains2 carbon atoms:

In another preferred embodiment, a cortistatin agent comprises acompound having a general structure corresponding to Formula IX:

Wherein:

W is the residuum of a saturated or unsaturated diol of 2 to about 12carbon atoms that has been reacted with a ketone group to form thedepicted ketal;

R¹ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur;

R⁴ is an acyl group COR, CO₂R, SO₂R, or P(O) (OR)₂ that contains 1 toabout 24 carbon atoms that can be a Ĉ-C₂4 straight chain, branched chainor cyclic alkyl, alkenyl, or alkynyl moiety, an aromatic, heterocyclicor alicyclic moiety, in which a heterocyclic moiety can contain 1 tofour rings that each contain up to four ring atoms other than carbonthat can be oxygen, nitrogen or sulfur; and,

R⁵ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur.

In another preferred embodiment, a cortistatin agent comprises acompound having a general structure corresponding to Formula X:

Wherein:

R¹ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; and

R⁵ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur.

In one embodiment, a cortistatin agent of Formula X comprises a compoundstructure corresponds to the Formula IV when W contains 2 carbon atoms:

In another preferred embodiment, a cortistatin agent comprises acompound having a general structure corresponding to Formula XI:

Wherein:

R¹ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; and,

R⁵ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur.

In one embodiment, a cortistatin agent comprises a compound having astructure corresponding to the Formula V:

In another preferred embodiment, a cortistatin agent comprises acompound having a general structure corresponding to Formula XII:

Wherein:

R¹ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur;

R⁵ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; and the circled X is a cyclic or heterocyclic substituent thatcontains 4 to about 15 carbon atoms, contains one to three saturated orunsaturated rings and up to three atoms per ring that are other thancarbon and can be oxygen, nitrogen or sulfur.

In one embodiment, the compound according to Formula XII wherein thecircled X group is aromatic.

In one embodiment, the cortistatin agent comprises a compound whosestructure corresponds to Formula VI:

In another preferred embodiment, a cortistatin agent comprises acompound having a general structure corresponding to Formula XIII:

Wherein:

R¹ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur;

R⁵ is hydrido (H), a straight chain, branched chain or cyclic alkyl,alkenyl, or alkynyl moiety, an aromatic, heterocyclic or alicyclicmoiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; and the circled X is a cyclic or heterocyclic substituent thatcontains 4 to about 15 carbon atoms, contains one to three saturated orunsaturated rings and up to three atoms per ring that are other thancarbon and can be oxygen, nitrogen or sulfur; with the proviso that R¹and R⁵ are not both methyl when the circled X group is a 7-isoquinoline.

In one embodiment, the compound according to Formula XIII wherein thecircled X group is aromatic. In one aspect, the circled X group is inthe β-configuration.

Thus, in one preferred embodiment, candidate agents which inhibitreplication of retroviruses, such as, for example, humanimmunodeficiency virus (HIV), comprises any one or more agents havingstructures corresponding to any one of Formulae I-XIII. These agentspreferably modulate retroviral transcription by modulating the functionor activity of a Trans-Activator of Transcription (Tat), aTransactivation Responsive element (TAR), a molecule associated withTrans-Activator of Transcription (Tat) (e.g. binds to Tat or modulatesthe function or activity of Tat), a molecule associated withTransactivation Responsive element (TAR) (e.g. binds to TAR or modulatesthe function or activity of TAR), and/or interaction between aTrans-Activator of Transcription (Tat) and a Transactivation Responsiveelement (TAR), or other molecules involved or associated withtranscription initiation and/or transcription of HIV in general.

In another preferred embodiment, candidate agents include any one ormore agents which can modulate retroviral replication and can beidentified by any number of ways. For example, in one embodiment, theagents are identified based on LTR-LacZ transactivation assays (cellsexpress a β-galactosidase (lacZ) gene driven by the 5′ LTR promoter ofHIV-1 and this reporter cell line is responsive to Tat protein expressedby an incoming virus), and secondly by RB-FRET (fluorescence resonanceenergy transfer) of the Tat-TAR interaction. The method used herein“RNA-binding mediated FRET (RB-FRET)” allows special and temporaldetection of specific RNA-protein complexes in living cells.

As discussed above, novel candidate agents can be substitutedcortistatin A molecules, see for example, Formulae I to XIII. The term“substituted” means that a group in question may be unsubstituted or itmay be substituted one or several times, such as 1 to 3 times or 1 to 5times. For example, an alkyl group that is “substituted” with 1 to 5fluoro atoms may be unsubstituted, or it may contain 1, 2, 3, 4, or 5fluorine atoms. Typically, substituted chemical moieties include one ormore substituents that replace hydrogen. Exemplary substituents include,for example, halo (e.g., F, Cl, Br, I), alkyl, cycloalkyl,alkylcycloalkyl, alkenyl, alkynyl, haloalkyl including trifluoroalkyl,aralkyl, aryl, heteroaryl, heteroarylalkyl, spiroalkyl, heterocyclyl,heterocycloalkyl, hydroxyl (—OH), alkoxyl, aryloxyl, aralkoxyl, nitro(—NO₂), cyano (—CN), amino (—NH₂), N-substituted amino (—NHR″),N,N-disubstituted amino (—N(R″)R″), carboxyl (—COOH), —C(═O)R″, —OR″,—C(═O)OR″, —C(═O)NHSO₂R″, —NHC(═O)R″, aminocarbonyl (—C(═O)NH₂),N-substituted aminocarbonyl (—C(═O)NHR″), N,N-disubstitutedaminocarbonyl (—C(═O)N(R″)R″), thiolato (SR″), sulfonic acid and itsesters (—SO₃R″), phosphonic acid and its mono-ester (—P(═O)(OR″)(OH) anddi-esters (—P(═O)(OR″)(OR″), —S(═O)₂R″, —S(═O)₂NH₂, —S(═O)₂NHR″,—S(═O)₂NR″R″, —SO₂NHC(═O)R″, —NHS(═O)₂R″, —NR″S(═O)₂R″, —CF₃, —CF₂CF₃,—NHC(═O)NHR″, —NHC(═O)NR″R″, —NR″C(═O)NHR″, —NR″C(═O)NR″R″, —NR″C(═O)R″and the like. In relation to the aforementioned substituents, eachmoiety “R” can be, independently, any of H, alkyl, cycloalkyl, alkenyl,aryl, aralkyl, heteroaryl, or heterocycloalkyl, or when (R″(R″)) isattached to a nitrogen atom, R″ and R″ can be taken together with thenitrogen atom to which they are attached to form a 4- to 8-memberednitrogen heterocycle, wherein the heterocycloalkyl ring is optionallyinterrupted by one or more additional —O—, —S—, —SO, —SO₂—, —NH—,—N(alkyl)-, or —N(aryl)-groups, for example. In certain embodiments,chemical moieties are substituted by at least one optional substituent,such as those provided hereinabove. In the present invention, whenchemical moieties are substituted with optional substituents, theoptional substituents are not further substituted unless otherwisestated. For example, when R¹ is an alkyl moiety, it is optionallysubstituted, based on the definition of “alkyl” as set forth herein. Insome embodiments, when R¹ is alkyl substituted with optional aryl, theoptional aryl substituent is not further substituted.

When any variable occurs more than one time in any constituent orformula for a compound, its definition at each occurrence is independentof its definition at every other occurrence. Thus, for example, if agroup is shown to be substituted with 0-2 substituents, then the groupmay optionally be substituted with up to two substituents and eachsubstituents is selected independently from the definition of optionallysubstituted defined above. Also, combinations of substituents and/orvariables are permissible only if such combinations result in stablecompounds.

When a bond to a substituent is shown to cross a bond connecting twoatoms in a ring, then such substituent may be bonded to any atom on thering having an attached hydrogen atom. When a substituent is listedwithout indicating the atom via which such substituent is bonded to therest of the compound of a given formula, then such substituent may bebonded via any atom in such substituent. Combinations of substituentsand/or variables are permissible only if such combinations result instable compounds.

In other embodiments, a cortistatin molecule may be chiral. The term“chiral” refers to molecules which have the property ofnon-superimposability of the mirror image partner, while the term“achiral” refers to molecules which are superimposable on their mirrorimage partner.

In other embodiments, a cortistatin molecule can be a stereoisomer. Theterm “diastereomers” refers to stereoisomers with two or more centers ofdissymmetry and whose molecules are not mirror images of one another.The term “enantiomers” refers to two stereoisomers of a compound whichare non-superimposable mirror images of one another. An equimolarmixture of two enantiomers is called a “racemic mixture” or a“racemate.” The terms “isomers” or “stereoisomers” refers to compoundswhich have identical chemical constitution, but differ with regard tothe arrangement of the atoms or groups in space.

Furthermore the indication of configuration across a carbon-carbondouble bond can be “Z” referring to what is often referred to as a “cis”(same side) conformation whereas “E” refers to what is often referred toas a “trans” (opposite side) conformation. Regardless, bothconfigurations, cis/trans and/or Z/E are contemplated for the compoundsfor use in the present invention. With respect to the nomenclature of achiral center, the terms “d” and “l”, “R” and “S”, configuration are asdefined by the IUPAC Recommendations. As to the use of the terms,diastereomer, racemate, epimer and enantiomer, these will be used intheir normal context to describe the stereochemistry of preparations.

Unless specifically stated herein, the cortistatin, cortistatinderivatives, cortistatin analogs, substituted cortistatin A and saltsthereof may contain any stereoisomer, racemate, or a mixture thereof.

In other embodiments, the cortistatin agent or molecule is labeled witha detectable moiety, including radionucleotides, enzymes, fluorescentagents, chemiluminescent agents, chromogenic agents, substrates,cofactors, inhibitors, magnetic particles, and the like.

In another preferred embodiment, the cortistatin molecule comprises alabel for detecting the molecule in vivo (e.g. for imaging or diagnosticpurposes) and/or to monitor the effects of the molecule during therapy.

In various embodiments, the cortistatin agents can be labeled with adetectable group. The detectable group can be any material having adetectable physical or chemical property. Such detectable labels havebeen well developed in the field of immunoassays and, in general, mostlabels useful in such methods can be applied to the present invention.Thus, a label is any composition detectable by spectroscopic,photochemical, biochemical, immunochemical, electrical, optical, orchemical means. In one embodiment, the CA is biotinylated. Thebiotinylated CA binds to streptavidin magnetic beads. Other usefullabels in the present invention include magnetic beads (e.g.,DYNABEADS™) which can be coated or conjugated to a desired molecule,fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red,rhodamine, and the like), radiolabels (e.g., ³H, ¹²⁵I, ³⁵S, ¹⁴C, or³²P), enzymes (e.g., horseradish peroxidase, alkaline phosphatase andothers commonly used in an ELISA), and colorimetric labels such ascolloidal gold or colored glass or plastic beads (e.g., polystyrene,polypropylene, latex, etc.).

In one embodiment, is a radiolabeled compound of any of the moleculesdelineated herein. Such compounds have one or more radioactive atoms(e.g., ³H, ²H, ¹⁴C, ¹³C, ³⁵S, ³²P, ¹²⁵I, ¹³¹I) introduced into thecompound. Such compounds are useful for drug metabolism studies anddiagnostics, as well as therapeutic applications.

In another embodiment, is a non-radiolabeled compound of the cortistatinmolecules delineated herein. Some examples of non-radioactive labelsinclude enzymes, chromophores, atoms and molecules detectable byelectron microscopy, and metal ions detectable by their magneticproperties.

In another embodiment, is an enzymatic-labeled compound of thecortistatin molecules delineated herein. Some useful enzymatic labelsinclude enzymes that cause a detectable change in a substrate. Someuseful enzymes and their substrates include, for example, horseradishperoxidase (pyrogallol and o-phenylenediamine), β-galactosidase(fluorescein β-D-galactopyranoside), and alkaline phosphatase(5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium). The useof enzymatic labels has been described in U.K. 2,019,404, EP 63,879, andby Rotman, Proc. Natl. Acad. Sci. USA, 47, 1981-1991 (1961).

In another embodiment, is a chromophore labeled compound of thecortistatin molecules delineated herein. Useful chromophores include,for example, fluorescent, chemiluminescent, and bioluminescentmolecules, as well as dyes. Some specific chromophores useful in thepresent invention include, for example, fluorescein, rhodamine, Texasred, phycoerythrin, umbelliferone, luminol.

In another preferred embodiment, the cortistatin molecules are labeledfor use in imaging. In imaging uses, the agents are labeled so that theycan be detected outside the body. Typical labels are radioisotopes,usually ones with short half-lives. The usual imaging radioisotopes,such as ¹²³I, ¹²⁴I, ¹²⁵I, ¹³¹I, ^(99m)TC, ¹⁸⁶Re, ¹⁸⁸Re, ⁶⁴Cu, ⁶⁷ _(Cu,)²¹²Bi, ²¹³Bi, ⁶⁷Ga, ⁹⁰Y, ¹¹¹In, ¹⁸F, ³H, ¹⁴C, ³⁵S or ³²P can be used.Nuclear magnetic resonance (NMR) imaging enhancers, such asgadolinium-153, can also be used to label the complex for detection byNMR. Methods and reagents for performing the labeling, either in thepolynucleotide or in the protein moiety, are considered known in theart.

The labels may be coupled directly or indirectly to the desiredcomponent of the assay according to methods well known in the art. Asindicated above, a wide variety of labels may be used, with the choiceof label depending on sensitivity required, ease of conjugation with thecompound, stability requirements, available instrumentation, anddisposal provisions.

Non-radioactive labels are often attached by indirect means. Generally,a ligand molecule (e.g., biotin) is covalently bound to the molecule.The ligand then binds to another molecules (e.g., streptavidin)molecule, which is either inherently detectable or covalently bound to asignal system, such as a detectable enzyme, a fluorescent compound, or achemiluminescent compound.

The molecules can also be conjugated directly to signal generatingcompounds, e.g., by conjugation with an enzyme or fluorophore. Enzymesof interest as labels will primarily be hydrolases, particularlyphosphatases, esterases and glycosidases, or oxidotases, particularlyperoxidases. Fluorescent compounds include fluorescein and itsderivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc.Chemiluminescent compounds include luciferin, and2,3-dihydrophthalazinediones, e.g., luminol. For a review of variouslabeling or signal producing systems that may be used, see U.S. Pat. No.4,391,904.

Means of detecting labels are well known to those of skill in the art.Thus, for example, where the label is a radioactive label, means fordetection include a scintillation counter or photographic film as inautoradiography. Where the label is a fluorescent label, it may bedetected by exciting the fluorochrome with the appropriate wavelength oflight and detecting the resulting fluorescence. The fluorescence may bedetected visually, by means of photographic film, by the use ofelectronic detectors such as charge-coupled devices (CCDs) orphotomultipliers and the like. Similarly, enzymatic labels may bedetected by providing the appropriate substrates for the enzyme anddetecting the resulting reaction product. Finally simple colorimetriclabels may be detected simply by observing the color associated with thelabel.

The present invention further encompasses salts, solvates, prodrugs andactive metabolites.

The term “salts” can include acid addition salts or addition salts offree bases. Preferably, the salts are pharmaceutically acceptable.Examples of acids which may be employed to form pharmaceuticallyacceptable acid addition salts include, but are not limited to, saltsderived from nontoxic inorganic acids such as nitric, phosphoric,sulfuric, or hydrobromic, hydroiodic, hydrofluoric, phosphorous, as wellas salts derived from nontoxic organic acids such as aliphatic mono- anddicarboxylic acids, phenyl-substituted alkanoic acids, hydroxyl alkanoicacids, alkanedioic acids, aromatic acids, aliphatic and aromaticsulfonic acids, and acetic, maleic, succinic, or citric acids.Non-limiting examples of such salts include napadisylate, besylate,sulfate, pyrosulfate, bisulfate, sulfite, bisulfite, nitrate, phosphate,monohydrogenphosphate, dihydrogenphosphate, metaphosphate,pyrophosphate, chloride, bromide, iodide, acetate, trifluoroacetate,propionate, caprylate, isobutyrate, oxalate, malonate, succinate,suberate, sebacate, fumarate, maleate, mandelate, benzoate,chlorobenzoate, methyl benzoate, dinitrobenzoate, phthalate,benzenesulfonate, toluenesulfonate, phenylacetate, citrate, lactate,maleate, tartrate, methanesulfonate, and the like. Also contemplated aresalts of amino acids such as arginate and the like and gluconate,galacturonate (see, for example, Berge, et al. “Pharmaceutical Salts,”J. Pharma. Sci. 1977; 66:1).

The phrase “pharmaceutically acceptable,” as used in connection withthose compounds, materials, compositions, and/or dosage forms that arewithin the scope of sound medical judgment, suitable for contact withthe tissues of human beings and animals without excessive toxicity,irritation, allergic response, or other problems or complicationscommensurate with a reasonable benefit/risk ratio. Preferably, as usedherein, the term “pharmaceutically acceptable” means approved by aregulatory agency of the federal or a state government or listed in theU.S. Pharmacopoeia or other generally recognized pharmacopeias for usein mammals, and more particularly in humans.

Typically, a pharmaceutically acceptable salt of a compound such as onedescribed herein or identified by the assays described, the compounds ofthe present invention may be prepared by using a desired acid or base asappropriate. The salt may precipitate from solution and be collected byfiltration or may be recovered by evaporation of the solvent. Forexample, an aqueous solution of an acid such as hydrochloric acid may beadded to an aqueous suspension of a compound of Formulae I to XIII andthe resulting mixture evaporated to dryness (lyophilized) to obtain theacid addition salt as a solid. Alternatively, a compound may bedissolved in a suitable solvent, for example an alcohol such asisopropanol, and the acid may be added in the same solvent or anothersuitable solvent. The resulting acid addition salt may then beprecipitated directly, or by addition of a less polar solvent such asdiisopropyl ether or hexane, and isolated by filtration.

The acid addition salts of the compounds may be prepared by contactingthe free base form with a sufficient amount of the desired acid toproduce the salt in the conventional manner. The free base form may beregenerated by contacting the salt form with a base and isolating thefree base in the conventional manner. The free base forms differ fromtheir respective salt forms somewhat in certain physical properties suchas solubility in polar solvents, but otherwise the salts are equivalentto their respective free base for purposes of the present invention.

Pharmaceutically acceptable base addition salts are formed with metalsor amines, such as alkali and alkaline earth metals or organic amines.Examples of metals used as cations are sodium, potassium, magnesium,calcium, and the like. Examples of suitable amines areN,N′-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine,dicyclohexylamine, ethylenediamine, N-methylglucamine, and procaine.

The base addition salts of said acidic compounds are prepared bycontacting the free acid form with a sufficient amount of the desiredbase to produce the salt in the conventional manner. The free acid formmay be regenerated by contacting the salt form with an acid andisolating the free acid.

Those skilled in the art of organic chemistry will appreciate that manyorganic compounds can form complexes with solvents in which they arereacted or from which they are precipitated or crystallized. Thesecomplexes are known as “solvates”. For example, a complex with water isknown as a “hydrate”. Solvates of the compound of the invention arewithin the scope of the invention. The salts of the Cortistatin A mayform solvates (e.g., hydrates) and the invention also includes all suchsolvates. The meaning of the word “solvates” is well known to thoseskilled in the art as a compound formed by interaction of a solvent anda solute (i.e., solvation). Techniques for the preparation of solvatesare well established in the art (see, for example, Brittain.Polymorphism in Pharmaceutical solids. Marcel Decker, New York, 1999.).Solvates may be represented, for example, by the formula R(solvent),where R is a compound of the invention. A given compound may form morethan one solvate including, for example, monosolvates (R(solvent)) orpolysolvates (R(solvent)_(n)) wherein n is an integer) including, forexample, disolvates (R(solvent)₂), trisolvates (R(solvent)₃), and thelike, or hemisolvates, such as, for example, R(solvent)_(n/2),R(solvent)_(n/3), R(solvent)_(n/4) and the like wherein n is an integer.Solvents herein include mixed solvents, for example, methanol/water, andas such, the solvates may incorporate one or more solvents within thesolvate.

The term “prodrug” includes compounds with moieties, which can bemetabolized in vivo. Generally, the prodrugs are metabolized in vivo byesterases or by other mechanisms to active drugs. Examples of prodrugsand their uses are well known in the art (See, e.g., Berge et al. (1977)“Pharmaceutical Salts”, J. Pharm. Sci. 66:1-19; Silverman (2004) TheOrganic Chemistry of Drug Design and Drug Action, Second Ed., ElsevierPress, Chapter 8, pp. 497-549). The prodrugs can be prepared in situduring the final isolation and purification of the compounds, or byseparately reacting the purified compound in its free acid form orhydroxyl with a suitable esterifying agent. Hydroxyl groups can beconverted into esters via treatment with a carboxylic acid. Examples ofprodrug moieties include substituted and unsubstituted, branch orunbranched lower alkyl ester moieties, (e.g., propionoic acid esters),lower alkenyl esters, di-lower alkyl-amino lower-alkyl esters (e.g.,dimethylaminoethyl ester), acylamino lower alkyl esters (e.g.,acetyloxymethyl ester), acyloxy lower alkyl esters (e.g.,pivaloyloxymethyl ester), aryl esters (phenyl ester), aryl-lower alkylesters (e.g., benzyl ester), substituted (e.g., with methyl, halogen, ormethoxy substituents) aryl and aryl-lower alkyl esters, amides,lower-alkyl amides, di-lower alkyl amides, and hydroxy amides. Otherprodrug moieties include propionoic and succinic acid esters, acylesters and substituted carbamates. Prodrugs which are converted toactive forms through other mechanisms in vivo are also included.

As used herein, the term “hydrate” refers to a compound of the presentinvention which is associated with water in the molecular form, i.e., inwhich the H—OH bond is not split, and may be represented, for example,by the formula R.H₂O, where R is a compound of the invention. A givencompound may form more than one hydrate including, for example,monohydrates (R—H₂O) or polyhydrates (R(H₂O)_(n)) wherein n is aninteger >1) including, for example, dihydrates (R(H₂O)₂), trihydrates(R(H₂O)₃), and the like, or hemihydrates, such as, for example,R(H₂O)_(n/2), R(H₂O)_(n/3), R(H₂O)_(n/4) and the like wherein n is aninteger.

As used herein, the term “acid hydrate” refers to a complex that may beformed through association of a compound having one or more basemoieties with at least one compound having one or more acid moieties orthrough association of a compound having one or more acid moieties withat least one compound having one or more base moieties, said complexbeing further associated with water molecules so as to form a hydrate,wherein said hydrate is as previously defined and R represents thecomplex herein described above.

A number of the compounds of the present invention and intermediatestherefor exhibit tautomerism and therefore may exist in differenttautomeric forms under certain conditions. As used herein, the term“tautomer” or “tautomeric form” refers to structural isomers ofdifferent energies which are interconvertible via a low energy barrier.For example, proton tautomers (also known as prototropic tautomers)include interconversions via migration of a proton, such as keto-enoland imine-enamine isomerizations. A specific example of a protontautomer is an imidazole moiety where the hydrogen may migrate betweenthe ring nitrogens. Valence tautomers include interconversions byreorganization of some of the bonding electrons. All such tautomericforms (e.g., all keto-enol and imine-enamine forms) are within the scopeof the invention. The depiction of any particular tautomeric form in anyof the structural formulas herein is not intended to be limiting withrespect to that form, but is meant to be representative of the entiretautomeric set.

Compounds described herein throughout, can be used or prepared inalternate forms. For example, many amino-containing compounds can beused or prepared as an acid addition salt. Often such salts improveisolation and handling properties of the compound. For example,depending on the reagents, reaction conditions and the like, compoundsas described herein can be used or prepared, for example, as theirhydrochloride or tosylate salts. Isomorphic crystalline forms, allchiral and racemic forms, N-oxide, hydrates, solvates, and acid salthydrates, are also contemplated to be within the scope of the presentinvention.

Certain acidic or basic compounds of the present invention may exist aszwitterions. All forms of the compounds, including free acid, free baseand zwitterions, are contemplated to be within the scope of the presentinvention. It is well known in the art that compounds containing bothbasic nitrogen atom and acidic groups often exist in equilibrium withtheir zwitterionic forms. Thus, any of the compounds described hereinthroughout that contain, for example, both basic nitrogen and acidicgroups, also include reference to their corresponding zwitterions.

The invention has been described in detail with reference to preferredembodiments thereof. However, it will be appreciated that those skilledin the art, upon consideration of this disclosure, may makemodifications and improvements within the spirit and scope of theinvention. Embodiments of the invention may be practiced without thetheoretical aspects presented.

All documents mentioned herein are incorporated herein by reference. Allpublications and patent documents cited in this application areincorporated by reference for all purposes to the same extent as if eachindividual publication or patent document were so individually denoted.By their citation of various references in this document, Applicants donot admit any particular reference is “prior art” to their invention.

EXAMPLES

The following non-limiting Examples serve to illustrate selectedembodiments of the invention. It will be appreciated that variations inproportions and alternatives in elements of the components shown will beapparent to those skilled in the art and are within the scope ofembodiments of the present invention.

Example 1 Potent Suppression of HIV Viral Replication 1 by a NovelInhibitor of Tat

Although treatment with antiretroviral drugs (ARVs) has extended thequality and expectancy of life for people infected with HIV, it has beenunsuccessful in curing HIV infection. ARVs fall into the following majorclasses: fusion inhibitors (FIs), nucleoside reverse transcriptaseinhibitors (NRTIs), non nucleoside reverse transcriptase inhibitors(NNRTIs), nucleotide reverse transcriptase inhibitors (NtRTIs), proteaseinhibitors (PIs) and integrase inhibitors (INIs). Highly activeantiretroviral therapy (HAART) is based on triple or quadruplecombinations of ARVs, however while reducing HIV to very low levels,this treatment fails to eliminate the infection completely.Ultrasensitive assays revealed that HIV persists in latently andproductively infected CD4⁺ T cells in the peripheral blood ofindividuals receiving HAART who have maintained undetectable plasmaviremia for prolonged periods of time. Residual viremia is not affectedby the addition of an integrase or a fusion inhibitor to a stable HAARTregimen suggesting that it originates from long-lived stable reservoirsthat contain an integrated provirus that continuously produces viralparticles despite HAART. Since viral production from these cellularreservoirs results from the continuous transcription of an integratedviral genome, they are not affected by NRTI, NNRTI, PIs, INIs or FIs.

The viral protein Tat, a potent activator of HIV gene expression, is apotential antiviral target. Tat is essential for the synthesis offull-length transcripts of the integrated viral genome by RNA polymeraseII (RNAPII). Tat mediates association between the host positivetranscription factor (pTEFb) complex and the trans-activation-responsiveelement (TAR) of the nascent viral RNA to promote transcriptionalelongation from the viral promoter.

Cortistatin A (CA) is a recently discovered natural steroidal alkaloidisolated from the marine sponge Corticium simplex, and it has beenreported to display anti-proliferative properties towards humanumbilical vein endothelial cells (HUVECs) with an average half maximalinhibitory concentration (IC₅₀) of 0.35 μM. The scarce natural supplyprompted the chemical synthesis of didehydro-Cortistatin A, theequipotent analog of Cortistatin A, starting from the inexpensive andabundant steroid prednisone and requiring only 13 steps for itssynthesis (FIG. 1A). This synthetic route provides gram quantities ofmaterial in a cost-effective manner.

Here it is reported that didehydro-Cortistatin A (dCA) potently andselectively inhibits Tat-mediated trans activation of the integrated HIVprovirus. dCA binds specifically to the TAR-binding domain of Tat and asa consequence, reduces cell-associated HIV-1 viral RNA and capsid p24antigen production in acutely and chronically infected cultured andprimary cells at an EC₅₀ as low as 0.7 pM. Moreover, in vitro dCAabrogates low-level virus replication from primary cells isolated frompatients undergoing HAART treatment. In total, these results define dCAas a novel anti-HIV drug that could decrease residual viremia duringHAART.

Materials and Methods

Cells: HEK293T and CEM SS were obtained from the American Type CultureCollection (ATCC). Human peripheral blood mononuclear cells wereobtained from the blood of healthy seronegative donors. HeLa,HeLa-CD4-LTR-Luc (PL11), HeLa-CD4-LTR-LacZ (P42), and HEK293T cells werecultured in DMEM supplemented with 5% FBS, L-glutamine (292 μg/ml) andantibiotics (100 units/ml penicillin and 100 μg/ml streptomycin). CEMSS, were cultured in Roswell Park Memorial Institut (RPMI) with 10%Fetalclonell (Hyclone) at 37° C. and 5% CO₂.

Viruses: HIV particles were initially prepared by transient transfectionof 293T cells with the proviral HIV-1 pNL4-3 DNA (Adachi A, et al. JVirol. 1986; 59(2):284-291) or ROD/A. Virus stocks for infections wereproduced by amplification of the virus by acutely infecting CEM SS cellswith HIV-1 pNL4-3 and concentration by ultracentrifugation of the cellsupernatant. Virus titers determined with HIV-1 p24 ELISA from AdvancesBioscience Laboratories.

Plasmids: pcDNA3.1 Tat-Flag-101 was generated by two-step PCR. The Tatsequence was amplified along with half of the Flag epitope via PCR andthis product was then used to add the remaining Flag sequence. The finalPCR product was cloned into pcDNA3.1-V5-HIS-B (Promega). pcDNA3.1Δ2-26-Tat-Flag-101 was generated by PCR amplification from pcDNA3.1Tat-Flag-101. pcDNA3.1 Tat-2-Flag-130 was generated using a similar two-step PCR approach as pcDNA3.1 Tat-Flag-101. NF-kB-Luc was purchased fromPromega (Cat No. E8491).

Recombinant Tat Protein: HIV-1 Tat protein, catalogue #2222 was obtainedthrough the NIH AIDS Research and Reference Reagent Program, Division ofAIDS, NIAID, NIH: HIV-1 Tat protein from Dr. John Brady and DAIDS,NIAID. GST-9G8 was purified using glutathion beads as previouslydescribed (Valente S T, et al., Mol Cell. 2009; 36(2):279-89).

Mitochondrial metabolic activity (MTT) Assay: MTT(3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay wasperformed on HeLa-CD4 cells in the presence of increasing concentrationsof dCA according to the manufacturer's protocol (ATCC).

Evaluation of toxicity by flow cytometry: PBMCs from HIV negativesubjects were incubated with increasing doses of dCA (0.1 dnM to 1 dμM).Viability was measured after 24 h and 72 h of culture. PBMCs werestained with FITC-labeled antibody to CD3 (555339), Alexa 700-labeledantibody to CD4 (557922), PerCP-Cy5.5-labeled antibody to CD8 (341051),V450-labeled antibody to CD14 (560349), V450-labeled antibody to CD19(560353), APC-labeled antibody to AnnexinV (550474) and Live/Dead Aquablue (L34957). All antibodies were purchased from BD Biosciences exceptfor Live/Dead Aqua blue (Invitrogen). Analyses were performed on a LSRII(BD Bioscience) flow cytometer.

Tat transactivation assay-CPRG: P42 cells were plated at 1×10⁴ cells perwell of 96 well. Twenty-four hours later HIV-1 pNL4-3 was added to thewells in the presence of testing compound or DMSO control in a totalvolume of 200 μL. Forty hours post infection cells were disrupted inlysis buffer (60 mM Na₂HPO₄, 40 mM NaH₂PO₄, 10 mM KCl, 10 mM MgSO₄, 2.5mM EDTA, 50 mM β-mercaptoethanol, 0.125% Nonidet P-40) and aquantitative chlorophenol red-β-D-galactopyranoside (CPRG)-based(Boehringer Mannheim) assay was performed. The cell extracts wereincubated in a reaction buffer (0.9 M phosphate buffer [pH 7.4], 9 mMMgCl₂, 11 mM β-mercaptoethanol, 7 mM CPRG) until a red color developed(from approximately 10 min to 4 h) and measured with an LP400 (BectonDickinson) plate reader at 572 nm. Experiments were performed intriplicate.

Isolation of primary Lymphocytes: To isolate PBMCs, 24 ml of total blooddiluted two fold in RPMI or PBS were carefully layered over 12 ml ofFicoll-paque and centrifuged at 2000 rpm for 20 min (brakes off).Resultant layers are approximately from top to bottom:plasma-platelets-PBMC-Ficoll-red blood cells (with granulocytes). Mostof the plasma was pipetted off and discarded. The buffy coat with PBMC'swas carefully removed from 3 large (50 ml) tubes and transferred to anew 50 ml tube. The remaining Ficoll and red blood cells were discardedin closed tubes. Enough PBS was added to the PBMCs to make up 50 ml andcentrifuged at 1200 rpm for 10 min, brakes on. The supernatant wasdecanted and the pellet was loosened and washed twice with PBS. Washedpellet was recovered in 30 ml of RPMI 1640 supplemented with 10% serum,1% Penicillin-streptomycin and mixed well. PBMCs were counted and platedat 1×10⁶ cells/ml. To activate the PBMCs, PHA (phytohaemagglutinin) wasadded at 3 μg/ml. Two to three days later add Interleukin 2 (IL2) at3×10⁻³ μg/ml.

Amplification of pNL4-3 in primary PBMCs: PHA activated PBMCs werecentrifuged and recovered at 6×10⁶ cells in 3 ml complete RPMI. Then 3ml of viral supernatant was added and incubated for 4 h at 37° C. Afterthis period, cells were centrifuged, washed 3 times with PBS andrecovered in 3 ml complete RPMI. PBMCs were plated at 0.5 ml per well ina 6-well plate, and 0.5 ml media with DMSO control or anti-viral controlat 2× final concentration was added. IL-2 was added at 3×10⁻³ μg/ml.Supernatant was recovered for p24 assay every 3-4 days post infection.Cells were split at 1×10⁶ cell per ml every 5-7 days.

HIV production in CD4 T cells from viremic and virally suppressedsubjects: All patients provided written informed consent, according tothe guidelines of the ethics committee of the Oregon Health and ScienceUniversity. CD4⁺T cells were isolated from PBMCs of HIV-infectedsubjects by negative magnetic selection (StemCell) and cultured for 9days in the presence of IL-2 (30 UI/mL), antiretroviral drugs (AZT (180nM), EFV (100 nM), RALT (200 nM)) and exposed to dCA 100 nM or 1 μM.Viral production was measured in the supernatant by a sensitive in-houseELISA specific for the viral capsid protein, p24. CD4⁺T cells fromvirally suppressed subjects were cultured for 9 days in the presence ofantiretroviral drugs (ARVs) and exposed to dCA 100 nM or 1 μM. Viralproduction was measured by quantification of viral particle-associatedRNA by ultra-sensitive two-step quantitative real-time reversetranscription-PCR (RT-qPCR). Briefly, viral particles in the cellculture supernatant were pelleted by centrifugation (60 min, 25000 g at4° C.). To generate the standard curve, a sample of LAI-HIV with knowntiter was pelleted in the same run. After centrifugation, viral RNA wasextracted with the QIAamp viral RNA extraction kit (Qiagen) according tothe manufacturer's instructions.

RT-qPCR of viral particles: Total viral RNA was reverse-transcribed intocDNA with gag gene-specific primers (25 pmol each), LM667 and GagRaccording to manufacturer's instructions (RT-PCR One Stepkit—Invitrogen). Pre-amplified products were diluted in DNase-RNase freewater, then subjected to quantitative real-time PCR on Rotor-Gene Q(Qiagen) in a reaction 25 pmol of the sense primer Lambda T, 25 pmol ofthe antisense primer AA55M, and 4 pmol of each hybridization probes (TIBMolBiol).

Cellular RNA Extraction: Cells were trypsinized and washed twice withPBS. Total RNA was extracted using the RNA extraction kit (Qiagen)following the manufacturers instruction.

Real-Time PCR: First-strand cDNA from RNA for qPCR was prepared usingSUPERSCRIPTIII™ first-strand cDNA kit (Invitrogen), following themanufacturer's instructions, using approximately 5 μg of RNA as startingmaterial and random hexamers as first-strand primers. Quantitative PCRwas performed with an aliquot of cDNA as template, using LIGHTCYCLER®480 SYBR Green I Master (Roche) in a 20 μL reaction according to themanufacturer's instructions. All reactions had a negative control inwhich no RT was added. The primers used were as follows:

5′GAPDH-(5′-CAACAGCCTCAAGATCATCAGCA-3′; SEQ ID NO: 1),3′GAPDH-(5′-AGGGATGACCTTGCCCACAGCCTTGG-3′; SEQ ID NO: 2),P1-(5′-GACAAGAGATCCTTGATCTGTGGAT-3′; SEQ ID NO: 3),P2-(5′-CCTTGTAGAAAGCTCGATGTCAGC-3′; SEQ ID NO: 4),P3-(5′-GGCTAACTAGGGAACCCACTG-3′; SEQ ID NO: 5),P4-(5′-CTGCTAGAGATTTTCCACACTGAC-3′; SEQ ID NO: 6),P5-(5′-TGTATCCTTTAGCTTCCCTCAGATCACTCTTTGGC-3′; SEQ ID NO: 7),P6-(5′-CCTTTTCCATTTCTGTACA-3′; SEQ ID NO: 8),P7-(5′-ACTTACGGGGATACTTGGGCAG-3′; SEQ ID NO: 9),P8-(5′-CTCCATTTCTTGCTCTCCTCTGTC-3′; SEQ ID NO: 10),P9-(5′-GAAAAACATGGAGCAATCACAAGTAGCAATACAG-3′; SEQ ID NO: 11),P10-(5′-CAGATCAAGGATATCTTGTCTTCTTTGGGAGTGAA-3′; SEQ ID NO: 12),GAPDH-Promoter-S: (5′-ATGGTTGCCACTGGGGATCT-3′; SEQ ID NO: 13),GAPDH-Promoter-AS: (5′-TGCCAAAGCCTAGGGGAAGA-3′; SEQ ID NO: 14),GAPDH-ORF-S: (5′-GGAGGTGGCCTAGGGCTGCTC-3′; SEQ ID NO: 15),GAPDH-ORF-AS: (5′-GGTGGAATCATATTGGAAC-3′; SEQ ID NO: 16).

RT-qPCR of viral particles: Total viral RNA (17 μL) was first treatedwith 1 unit DNase I (Invitrogen) for 10 min at 25° C. followed by DNaseI inactivation with 1 μL 25 mM EDTA for 10 min at 65° C. Total viral RNAwas then reverse-transcribed into cDNA for quantitative PCR analysis.RT-PCR was performed in a final volume of 50 μL containing 22 μL ofDNase I treated RNA, gag gene-specific primers (25 pmol each), LM667(5′-ATG CCA CGT AAG CGA AAC TCT GGC TAA CTA GGG AAC CCA CTG-3′; SEQ IDNO: 17) and GagR (5′-AGC TCC CTG CTT GCC CAT A-3′; SEQ ID NO: 18) and 2μL of Superscript III RT/Platinum Taq mix (RT-PCR One Stepkit—Invitrogen). Cycling conditions included reverse transcription (50°C. 30 min) followed by denaturation (94° C. 2 min), 20 cycles ofamplification (94° C. 15 s, 62° C. 30 s, 68° C. 60 s) and a finalelongation step (68° C. 5 min). The pre-amplified products were diluted(1:10) in DNase/RNase-free water, then subjected to quantitativereal-time PCR on Rotor-Gene Q (Qiagen) in a 25 μl reaction containing2×Rotor-Gene Probe PCR mix (Qiagen), 25 pmol of the sense primer LambdaT (5′-ATG CCA CGT AAG CGA AAC-3′; SEQ ID NO: 19), 25 pmol of theantisense primer AA55M (5′-GCT AGA GAT TTT CCA CAC TGA CTA A-3′; SEQ IDNO: 20), and 4 pmol of each hybridization probes 5′-CAC AAC AGA CGG GCACAC ACT ACT TGA-3′-fluorescein (SEQ ID NO: 21) and LCred640-5′-CAC TCAAGG CAA GCT TTA TTG AGG C-3′-phosphate (SEQ ID NO: 22) (TIB MolBiol).The cycling conditions included an initial denaturation (95° C. 4 min),followed by 35 cycles of amplification (95° C. 10 s, 60° C. 10 s, 72° C.9 s). Results were analyzed by using the RotorGene software (Qiagen).

Transfection and protein extraction: HEK293T cells were transfected with10 μg of the empty vector control pCDNA4, pFI-Tat-Flag-86WT or pCDNA3.19G8-Flag. Forty-eight hours post transfection, cells were washed twicewith PBS and disrupted on ice with lysis buffer [20 mM Hepes (pH 7.4),100 mM KCl, 0.2 mM EDTA, 5 mM β-mercaptoethanol, 0.1% IGEPAL CA-630, 10%glycerol and complete EDTA-free protease inhibitor cocktail (Roche)].After centrifugation at 10000 g for 10 min at 4° C., supernatants werecollected and protein concentration was determined by Bradford assayaccording to the manufacturer's instructions (Bio-Rad).

Bio-dCA pull-down: DYNABEADS® MYONE™ Streptavidin T1 (12.5 μl slurry)(Invitrogen) were pre-saturated with 1.88 μl of 1 mM in DMSO of Biotinalone or Bio-dCA and incubated for 1 h at room temperature with orbitalrocking, plus an additional 30 min with Biotin (0.63 μl of 1 mM inDMSO). Protein extracts (250 μg per sample) were incubated with thepre-saturated beads in lysis buffer supplemented with 0.1% BSA for 1 hat 4° C. with orbital rocking. After incubation, the beads were washedthree times with lysis buffer. To elute the cellular proteinsinteracting with dCA, the beads were boiled 3 min in 2X Elution buffer[125 mM Tris-HCl (pH 6.8), 4% SDS, 5 mM β-mercaptoethanol, 20% glycerol,0.004% Bromophenol Blue].

For the pull-down of recombinant Tat (#2222 of NIH) and GST-9G8,streptavidin-agarose beads (40 μl slurry) were pre-saturated with 1.5 μlof 1 mM in DMSO, Biotin alone, or Bio-dCA and incubated for 1 h at roomtemperature. Recombinant proteins were pre-incubated 10 min with DMSO,dCA, or Raltegravir in binding buffer (PBS 100 mM pH 7.3, 150 mM NaCl,BSA 0.1%, IGEPAL CA-630 0.001%) and then added to the beads for 1 h at4° C. After incubation, the beads were washed three times with PBS andproteins were eluted as before.

Western blot analysis: Cells were lysed in lysis buffer [20 mM Hepes (pH8.0), 100 mM KCl, 0.2 mM EDTA, 5 mM β-mercaptoethanol, 0.1% IGEPALCA-630, 10% glycerol and complete EDTA-free protease inhibitor cocktail(Roche)]. The lysate was centrifuged at 12,000 g for 5 min at 4° C. andthe resulting supernatant was boiled in 6X SDS loading buffer. Theprotein extracts were separated by SDS-PAGE and transferred onto apolyvinylidene fluoride membrane. Membranes were probed with ananti-CDK11 (P2N) rabbit polyclonal antibody 1:1000, an anti-Flag M2mouse monoclonal antibody 1:5000 (Sigma), an anti-GST rabbit polyclonalantibody 1:2000 (Bethyl), and/or an anti-ABCE1 (ab32270) rabbitpolyclonal antibody 1:1000 (Abcam). The membranes were incubated inhorseradish peroxidase-conjugated anti-mouse or anti-rabbit IgG goatpolyclonal antibodies as secondary antibodies. Bands were visualizedusing the ECL Western blotting system (Amersham).

Luciferase Assay-Effect of Cortistatin A on TNF-α activation of an NF-kBreporter construct: TE671 cells were plated at 6.25×10⁴ per well in a24-well plate. Cells were transfected twenty-four hours later witheither 200 ng or 400 ng of NF-kB-Luc (Promega, Cat No. E8491) usingFugene 6 (Roche) per manufacturer's instruction. The next day cells weresplit equally into two new wells and treated with TNF-α (30 ng/ml)and/or dCA (1 μM). Cells were lysed 5 hours later with 1X Lysis Bufferand luciferase activity was measured using the luciferase Assay System(Promega) on a Berthhold luminometer. Protein concentration wasdetermined by Bradford assay. Results corresponding to the adjustment ofthe luciferase activity per protein concentration of each sample areshown as Relative light units (RLU). Experiments were performed intriplicate.

Tat Transactivation assay: PL11 cells were plated at 1×10⁵ cells perwell in a 6 well plate. The following day recombinant Tat protein (AIDSResearch and Reference Reagent Program, Cat No. 11882) at 5 μg/ml and/orCortistatin A at increasing concentrations were added to the cells, inculture media without serum and in the presence of 100 μM of chloroquine(increases Tat uptake). Five hours later, serum was added at 5% to theculture media. Forty hours later cells were lysed with 1X Lysis Bufferand luciferase activity was measured as before. Protein concentrationwas determined by Bradford assay. Results corresponding to theadjustment of the luciferase activity per protein concentration of eachsample are shown as RLU.

In vitro kinase assay: Sixty ng of purified CDK11 wild-type (WT) ormutant (DN) were added to 2 μg of purified 9G8 in kinase buffer [50 mMTris-HCl (pH 7.9), 20 mM MgCl2] and incubated 30 min on ice with dCA orthe equivalent of DMSO. To the mixture, 100 μM of ATP and 5 μCi ofγ-³²P-ATP (3000 Ci/mmol 10 mCi/ml) were added to a final volume of 30 μlin kinase buffer. Following 30 min at 30° C., the reaction wasterminated by addition of 6 μl of 6X SDS loading buffer. After boilingfor 10 min, proteins were separated by SDS-PAGE. The gel was dried andvisualized by autoradiography.

Chromatin immunoprecipitation (ChIP) assay: HeLa-CD4 cells chronicallyinfected with pNL4-3 were seeded in 15 cm plates at 1×10⁶ cells andtreated 4-5 days with DMSO or dCA [0.1 and 10 nM] and 6-8 h withFlavopiridol [50 nM]. Cells were fixed with formaldehyde (1% [vol/vol])to crosslink the chromatin and incubated at room temperature for 10 min.Cross-linking was arrested by adding glycine [0.125 M] and incubated foran additional 5 min at room temperature. Cells were then pelleted,washed twice with phosphate-buffered saline, ressuspended in SDS lysisbuffer, and incubated 10 min on ice. All solutions used prior to thecollection of chromatin-antibody complexes contained protease andphosphatase inhibitor cocktail. Cell lysates were sonicated 4 times for10 s bursts on ice. The sheared chromatin was diluted by the addition of3 volumes of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mMEDTA, 16.7 mM Tris-HCl (pH 8.1), 167 mM NaCl) and pre-cleared withsalmon sperm DNA-protein A/G agarose slurry for 2 h. Beads were removedby centrifugation, 10% of the pre-cleared chromatin supernatant wasremoved to serve as the pre-IP (‘input’) control, and the remainingpre-cleared chromatin was incubated with either 10 mg/ml of anti-RNAPII(Millipore #05-623) or non-specific rabbit IgG (Bethyl #P120-301)overnight. Chromatin-antibody complexes were collected by incubationwith salmon sperm DNA-protein A/G agarose (50% slurry) and subsequentcollection of beads by centrifugation. Bead pellets were washed inlow-salt (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.0),150 mM NaCl), high-salt (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mMTris-HCl (pH 8.0), 500 mM NaCl), and LiCl (0.25M LiCl, 1% NP-40, 1% SDS,1 mM EDTA, 10 mM Tris-HCl pH 8.0) immune complex wash buffers followedby two washes with TE buffer. Antibody-chromatin complexes were elutedfrom the beads by incubation with elution buffer (0.1% SDS, 0.1 MNaHCO₃). NaCl was added to eluates (final concentration of 0.2 M) andincubated at 65° C. for 4-6 h. The samples were then treated with RNaseA and proteinase K, and the DNA was purified using the Qiaquick PCRpurification kit (Qiagen) or by phenol/chloroform extraction followed byethanol precipitation. The pre-IP input sample was purified in a mannersimilar to the bound ChIP fraction described above. Immunoprecipitated(IP) (2 μl) or input 10% (diluted 1:20) DNA was used in 20 μl qPCRmixtures with primers: P1(-426) and P2(-126) (LTR promoter), P5(1782)and P6(2207) (ORF pNL4-3). Primer sequences are shown above. A fractionof input was used to standardize the values obtained. The relativeproportions of co-immunoprecipitated DNA fragments were determined onthe basis of the threshold cycle (CT) for each PCR product.

The data sets were normalized to input values (percent input;2CT(input)-CT(IP) 100).

Immunofluorescence: HeLa cells were grown on fibronectin treatedcoverslips and transfected with the indicated plasmids. Followingtransfection, cells were treated with DMSO or dCA. Cells were then fixedwith 3.7% formaldehyde. After fixation, the cells were permeabilizedwith 0.1% triton X-100 in PBS with 5% FBS. Primary antibodies (mouseα-FLAG M2 (Sigma), rabbit α-Fibrillarin C13C3 (Cell Signaling), and/orrabbit α-Cyclin T1 H-245 (Santa Cruz)) were added along with thepermeabilization solution and incubated at room temperature for 1 hour.The cells were washed with PBS and incubated with 1:500 dilution ofAlexa Fluor conjugated secondary antibodies in PBS containing 5% FBS for1 hour in the dark. Following washing with PBS, the cells were placed onglass slides using mounting media containing DAPI and the coverslipswere sealed for imaging on the FluoView FV 1000 laser scanningmicroscope.

Synthesis of biotinylated dCA: Compound 1-2 (4 mg, 5.7 μmol) and 3 (4mg, 12 μml) were dissolved in CH₂Cl₂:DMSO 10:1 (0.55 ml, 0.01 M). Tothis solution were added EDC (2.6 mg, 17 μmol, 3 equiv) and DMAP (1 mg,9 μmol, 1.5 equiv). The reaction mixture was stirred at room temperaturefor 12 h, at which point it was quenched with sat. aq. NaHCO₃ (5 ml).The aqueous layer was extracted with EtOAc (4×5 ml). The combinedorganics were dried with MgSO₄, filtered, and concentrated in vacuo. Theresidue was then purified by HPLC, yielding 1a (1.2 mg, 25%) and 1b (1.7mg, 25%) as a colorless oil.

Results

Didehydro-Cortistatin A Inhibits HIV transcriptional activity:Eukaryotic initiation factor 3 subunit f (eIF3f) mediates restriction ofHIV-1 RNA 3′ end-processing through the involvement of a set of factorsthat includes eIF3f, the SR protein 9G8, and cyclin-dependent kinase II(CDK11) (Valente S T, et al., (2009) Proc Natl Acad Sci USA 106,4071-4078; Valente S T, et al., (2009) Mol Cell 36, 279-289). These dataevidenced that a CDK11 inhibitor might possess anti-HIV activity. Giventhat Cortistatin A is a high affinity CDK11 ligand, the ability of itsanalog dCA to decrease HIV production by interfering with CDK11 activitywas examined. While an effect of dCA on CDK11 activity was notconfirmed, a potent activity as an inhibitor of HIV-1 transcription wasidentified.

HIV-1 susceptibility to dCA was assayed using a reporter cell line thatstably expresses β-galactosidase (LacZ) gene; LacZ expression is drivenby the 5′ long terminal repeat (LTR) promoter of HIV-1 and responds toTat expressed by an incoming virus. HeLa-CD4-LacZ cells were infectedwith HIV-1 at different multiplicities of infection (MOIs) in thepresence of increasing concentrations of dCA and β-gal activity wasdetermined 48 h post infection (FIG. 1B). Inhibition of transcriptionwas dose-dependent, with an EC₅₀ as low as 2.6 nM at the highest, and0.7 pM at the lowest MOI; the lower MOI is more representative ofbiological amounts of virus found in infected subjects. Pre-treatment ofcells with dCA for 24 h prior to infection resulted in a 7-foldreduction in the EC₅₀ (FIG. 1C), evidencing that dCA 92 potency dependson the time of addition or target concentration. Following acuteinfection, maximal inhibition leveled off at 75-85%, possibly due to theinability of dCA to block Tat-independent HIV transcription.Transcription of the HIV-1 provirus is regulated by both viral andcellular transcription factors. Before Tat is produced, low-level basaltranscription from the viral promoter is initiated by cellular factors,such as the nuclear factor-kappa B (NF-kB), Sp1, TATA-binding proteinand RNAPII. A desirable Tat inhibitor should block Tat-mediatedactivation of the viral promoter without affecting its basaltranscription, which would result in cellular toxicity, given the sharedtranscription factors of the HIV promoter and cellular genes. Theeffective concentrations of dCA did not compromise HeLa-CD4 cellviability, as a half-maximal cytotoxic concentration (CC50) of 20 μM(FIG. 7) was observed.

To assess whether the viral block mediated by dCA occurs before or afterintegration of proviral DNA into the host cell chromosome, HeLa-CD4cells were infected with HIV-1, treated with different concentrations ofdCA and total cellular DNA was extracted 24 h later for quantificationof proviral DNA by real time quantitative PCR (qPCR). Such an early timepoint rules out de novo infections. The presence of dCA did not changeintegrated HIV DNA copy number as compared with DMSO-treated cells (FIG.1D). These results are consistent with a viral block by dCA at a stepfollowing-integration of the provirus into the host chromosome. ViralmRNA expression in cells treated with increasing concentrations of dCAwas then measured by reverse transcription (RT) qPCR. A drasticdose-dependent reduction in the total amount of viral RNA in infectedcells was detected (FIG. 1E), further evidencing that dCA inhibitstranscription from the integrated viral promoter. This conclusion wasfurther supported by the fact that treatment of cells that werechronically infected, and therefore continuously shedding the virus(without incurring new infections, due to down-regulation of CD4 fromthe cell surface), reduced virus production to undetectable levels (FIG.1F).

Treatment of chronically HIV-1 infected HeLa-CD4 cells with dCA for 10or 60 days resulted in a drastic reduction of viral cellular RNA levelswith an EC₅₀ as low as 0.1 nM and an EC₉₀ of less than 10 nM (FIG. 1F).Moreover, a continuous reduction in viral RNA levels was observed in thecell with increased treatment times with dCA, an expected result sinceTat inhibition decreases Tat production. Results were similar when viralrelease from cells treated for 60 days were measured by p24enzyme-linked immunosorbent assay (ELISA) (FIG. 1G). Furthermore dCA,but not other ARVs, reduced viral RNA levels in the lymphocytic cellline CEM SS chronically infected with pNL43 (FIG. 1H), demonstratingthat the effect of dCA is not only cell-type independent but also thatthey extend to the reduction of viral expression from cells alreadyinfected, a result that none of the currently used ARVs is able toachieve.

Didehydro-Cortistatin A is a Tat inhibitor: To determine whether dCAdirectly impacts Tat-mediated transcriptional activation from the viralpromoter, a reporter system solely dependent on Tat activity was used.Recombinant Tat protein was added in the presence or absence of dCA toHeLa-CD4 cells stably expressing a construct containing the HIV-1 5′LTRpromoter driving luciferase expression (LTR-Luc). Transcriptionalrepression was observed only in the presence of dCA (FIG. 2A). Similarresults were obtained when a Tat-encoding plasmid was transfected intoHeLa-CD4 expressing LTR-Luc (FIG. 2B). These results evidence that dCAblocks Tat transcriptional activation of the HIV-1 promoter. Reportertranscription from heat-inactivated recombinant Tat protein (FIG. 2A),which was used as negative control, reflects Tat-independent activationof the HIV promoter, and accounts for approximately 20% of maximalactivation. This result supports the notion that the observed maximuminhibition plateau at 75-85% during acute infection is due toTat-independent activity of the promoter. In line with these results,dCA did not alter basal transcription from the LTR promoter in theabsence of Tat, nor when Phorbol 12-Myristate 13-Acetate (PMA) was usedto activate promoter transcription via NF-kB (FIG. 2A). Furthermore, dCAshowed no effect on TNFα activation of an NF-κB reporter construct (FIG.8B), showing that inhibition by dCA is independent of NF-κB.Transcription from CXCR4, herpes simplex thymidine kinase (TK),phosphoglycerate kinase (PGK) or CD4 promoters was also not affected bydCA (FIGS. 8C, 8D).

Tat is a 14 kDa, 101 residue protein with several functional domains(FIG. 2C). Domains II and III are essential for transactivation anddomain IV mediates TAR RNA binding and nuclear localization. An 86-aminoacid form of Tat (encompassing residues 1-86) is produced in a fewlaboratory-passaged virus strains and has been frequently used to studyTat. To determine whether Tat binds dCA a biotinylated form of thecompound (Bio-dCA) (FIG. 2D) was synthesized. Notwithstanding, that thisderivative displayed a tenfold higher EC₅₀ than dCA, at higherconcentrations showed the same efficacy and did not compromise theviability of the cells (FIGS. 9A, 9B). Bio-dCA coupled tostreptavidin-coated magnetic beads retained flag-tagged Tat (86 a.a.) orTat (101 a.a.) transiently expressed in cells, but not a basic regionTat mutant (Tat-1 BRM) that no longer binds TAR and was thereforetransactivation-incompetent (FIGS. 2C, 2E). Bio-dCA did not interactwith the RNA-binding protein 9G8, ABCE1 protein (used as negativecontrols), nor with CDK11, which had been reported to interact with itsanalog CA in vitro. In line with the lack of interaction between dCA andCDK11, dCA was unable to block in vitro CDK11 kinase activity, andfailed to alter the cellular expression profile of CDK11 (FIGS. 10A,10B). In summary, an interaction between dCA and CDK11 was not found aspossibly expected from the report suggesting an interaction betweenCDK11 and CA (Cee V J, et al., (2009) Angew Chem Int Ed Engl 48,8952-8957).

To confirm that Bio-dCA interacts directly with Tat pull-downexperiments were performed with recombinant purified protein (FIG. 2F).Recombinant Tat protein bound directly to Bio-dCA and was competed by CAbut not by Raltegravir, used as negative control, demonstrating thespecificity of the interaction. As expected, Bio-dCA did not associatewith purified recombinant 9G8 used as negative control.

While it is well known that Tat accumulates in the nucleolus via itsbasic region, Tat function in this compartment is still largely unknown.The nucleolus, a highly organized, non-membrane-bound-subcompartment, isinvolved in transcription and maturation of rRNA and ribosome biogenesisas well as in apoptosis and cell cycle contro. Some studies suggest thatthe nucleolus plays a role in HIV-1 infection. First, lymphocytesisolated from infected patients show abnormal nucleolar structure, andsecond, nucleolar localization of TAR impairs virus replication.

Given that dCA interacts with Tat via its basic domain, which is alsothe nucleolar localization signal (NoLS), it was questioned whether dCAimpacts Tat localization. To address this possibility, HeLa-CD4 cellswere transfected with a plasmid expressing Tat-flag and assessed Tatlocalization in the presence or absence of dCA by fluorescencemicroscopy upon immunostaining with an anti-flag antibody (FIG. 2G). dCAcaused a redistribution of Tat to the periphery of the nucleolus,forming a distinctive ring-like structure (FIG. 2G), in a dose-dependentmanner (FIG. 11A). The Tat basic mutant was analyzed in parallel, andthis protein was completely excluded from the nucleolus both in thepresence or absence of dCA. The effect of dCA on wild-type Tat appearsto mimic the phenotype caused by the basic domain mutation (FIG. 2G andFIG. 11B). The Δ2-26-Tat mutant lacks the transactivation domain butretains the basic domain and shows a predominantly nucleolarlocalization. In the presence of dCA, this mutant was like wild-typeTat, excluded from the nucleolus, consistent with the presence of thebasic domain (FIGS. 11B, 11C). The localization of fibrillarin, acomponent of small nucleolar ribonucleoproteins (snoRNPs) or of cyclinT1, a Tat-binding protein, was not altered by dCA (FIGS. 11A, 11B, 11C).The biotinylated form of dCA had the same effect on Tat localization(FIG. 11D). As Tat localizes to the nucleolus via the basic region,these results support the biochemical data showing a direct interactionof dCA with Tat via the TAR binding domain.

Didehydro-Cortistatin A blocks transcriptional initiation/elongation:p-TEFb is composed of cyclin T1 and cyclin-dependent kinase 9 (CDK9) andis recruited by Tat to the HIV TAR region. pTEFb is used at manypromoters, including HIV-1, to phosphorylate serine 2 residues presentin the RNAPII C-terminal domain (CTD), converting a nonphosphorylated toa hyperphosphorylated RNAPII form that engages in productive elongation.The effects of dCA on transcription initiation and elongation from the5′LTR by RNAPII were analyzed by qRT-PCR and chromatinimmunoprecipitation (ChiP).

For these studies, the amounts of viral RNA present at differentdistances from the promoter were measured using sets of oligonucleotideprimer pairs specific to quantify transcripts made up to 100 bp, 5.3 kbor 8.5 kb from the transcription start site (FIG. 3A). It was observedthat even in the absence of drug, elongation from the HIV-1 viralpromoter is not very efficient. In the presence of DMSO alone only 30%of 5.3 kb long transcripts and 6% of 8.5 kb long transcripts wereproduced (FIG. 3B—left panel). The addition of dCA further decreased theproduction of longer viral RNA species in a dose-dependent manner (FIG.3B), supporting the notion that dCA inhibits elongation from the viralpromoter.

Using chromatin immunoprecipitation (ChiP) with an anti-RNAPII antibodyand qPCR, the effect of dCA on RNAPII occupancy of the 5′LTR promoter orviral ORF in HeLa-CD4 cells chronically infected with HIV-1 pNL43 wasmeasured with the indicated primers (FIG. 3A). Association of RNAPIIwith the HIV promoter and ORF was significantly decreased in thepresence of dCA, in a dose-dependent manner, while the occupancy of theGAPDH promoter and ORF was not affected (FIG. 3C and FIG. 12).Flavopiridol (Flay), a CDK9 inhibitor, was used as a positive controland DMSO served as negative control. These results provide evidence thatdCA might block not only elongation but also initiation of transcriptionin chronically infected cells. As transcription is reduced and less Tatprotein is made, the LTR promoter would tend to shut off with time,leading to reduced initiation. Furthermore, dCA might reduce Tatmediated recruitment of chromatin-remodeling proteins, such as thehistone acetyltransferases (HATs) p300/CBP, to the promoter region.Together these results clearly show dCA's ability to inhibit RNAPIItranscription from the HIV-1 provirus.

To determine whether virus production by cells treated with dCA reboundsafter withdrawal of the drug, HeLa-CD4 cells chronically infected withpNL43 for 2 months were treated with dCA and viral RNA levels weremeasured by qRT-PCR at several time points after terminating treatment.No virus rebound was observed even 27 days after the treatment wasstopped (FIGS. 4A, 4B), contrary to what is normally observed with ARVs.Overall, these provide evidence that dCA promotes rapid and permanentsilencing of the HIV promoter, which may drastically limit the emergenceof dCA-resistant viruses.

Potency and Scope of Didehydro-Cortistatin A Inhibition: The potency ofdCA inhibition was compared with that of nine compounds from four majorARVs (FIGS. 5A-5D). In a two-day acute infection assay withHeLa-CD4-LTR-LacZ cells, dCA exhibited a 1.5-3 log lower EC₅₀ than allother ARVs. Although dCA only reduces infectivity by 75-80% (versus95-100% for the NNRTIs and INIs) this value is comparable to the NRTIsand is better than the PIs (˜30%). PIs show low efficacy in this short48 h assay as they act only upon spreading from the initial infection.Given that dCA blocks a post-integration event, this result isunsurpassing and it compares favorably with late acting compounds suchas PIs. The results were similar when viral production was determined byRT-PCR of viral RNA in HeLa-CD4 cells infected and treated for four dayswith one compound from each class of inhibitors (FIG. 5E). Again, dCAconsistently showed lower EC₅₀ values (<0.1 nM) with maximum inhibitionaround 80% while other ARVs showed complete inhibition, albeit with 100fold or higher EC₅₀.

The susceptibility of HIV-2 to dCA inhibition was tested. dCA inhibitedacute infection of HeLa-CD4 cells by HIV-2 (ROD/A) with an EC₅₀ of ≈5 nM(FIG. 5F), as well as chronic infection with an EC₅₀ of ≈1.7 nM (FIG.5G), demonstrating the broad potential of dCA. Furthermore, dCA excludedequally well HIV-2 Tat protein from the nucleolus (FIGS. 11B, 11C). Theslightly lower efficiency of dCA in blocking HIV-2 replication ascompared to HIV-1 might be explained by the fact that unlike the HIV-1TAR element, which contains a single stem-loop, the HIV-2 TAR elementconsists of 2 characteristic stem-loop structures, both of whichparticipate in optimal Tat response.

Didehydro-Cortistatin A inhibits HIV replication in primary cells fromuninfected and infected subjects at different disease stages: Theability of dCA to inhibit HIV-1 replication was measured in freshlyisolated uninfected human peripheral blood mononuclear cells (PBMCs)stimulated with mitogen phytohaemagglutinin (PHA) and interleukin 2(IL-2). PBMCs were infected with pNL43 and treated with raltegravir,saquinavir or dCA, and viral replication measured by p24 ELISA. dCAinhibited replication with an EC₅₀ of <1 nM (FIGS. 5H, 5I) in primarycells similar to that obtained with raltegravir and saquinavir, howevera maximum inhibition plateau of 86% was observed for dCA. dCA treatmentof primary cells did not affect cell viability, as the CC₅₀ values was100 μM, which is higher than what was observed for Hela-CD4 cells (FIGS.13A, 13B). HIV-1 transcription is intimately linked to T-cell activationdue to shared motifs between the HIV-LTR and the regulatory regions ininduced genes, namely NF-κB. A large variety of T cell stimuli activateNF-κB, including PHA, IL-2 and tumor necrosis factor alpha (TNF-α). Inthe absence of Tat-independent promoter activity, such as the activationmediated by NF-κB, dCA inhibition of HIV replication would be expectedto be higher.

The potency of dCA was further tested on spontaneous viral output (p24production) from primary CD4⁺ T cells isolated from five viremicHIV-infected patients (FIG. 6A). Cells were grown in IL-2 to increaseviability. With ARVs alone, which inhibit all new infections, decreasedviral production by approximately 25% was observed, and addition of dCAto the ARVs further decreased p24 production by another 20%. dCA thusprovides an important additive effect with other ARVs when added toprimary CD4⁺ T cells from HIV-viremic subjects.

Also investigated was whether dCA could impact residual viremia fromvirally suppressed subjects (plasma viral load less than 50 copies/mL)receiving HAART. CD4⁺T cells were isolated from PBMCs of four subjectstreated for at least 3 years who spontaneously released viral particlesin vitro and grew them in the absence of IL-2. Using an ultrasensitiveRT-PCR assay, in the presence of ARVs, a reduction of viral productionof 99.7% at day 6 was observed (FIG. 6B). Importantly, dCA did notaffect the viability of the cells at the concentrations used.Altogether, these results provide evidence that dCA is a highly potentinhibitor of the residual viral production from CD4⁺T cells of virallysuppressed subjects. These results also support the prediction thathigher HIV-1 inhibition by dCA is observed in the absence of promoteractivation by IL-2 (mediated by NF-κB), when replication is mostlydependent on Tat activity.

Didehydro-Cortistatin A pharmacokinetics: To evaluate the in vitro andin vivo stability of dCA an analytical LC-MS/MS method was developed(Table 1). In vitro studies compared murine and human hepatic microsomes(150 donor mixed male/female pool). Sunitinib, an FDA-approved kinaseinhibitor with favorable human pharmacokinetics, was included as apositive control. dCA was resistant to hepatic oxidative metabolism inboth human and mouse (Table 1A). Based on the encouraging microsomaldata, follow-up mouse experiments were conducted to evaluate the abilityto dose dCA via oral gavage (PO) and intraperitoneal injection (IP). dCAwas easily formulated (1 mg/mL in water) due to its high aqueoussolubility. C57B16 mice were dosed at 10 mg/kg and drug levels werequantitated in plasma at 1, 6, and 24 h by LC-MS/MS (Table 1B). Theresults impressively demonstrated that dCA can be given either IP ororally. Drug levels at 1 h after dosing were greater than 1000-fold theEC₅₀ value found in the cell-based assays. dCA concentration decreasedat 6 and 24 h, but even 24 h post dose, plasma drug levels for all micewere above 30 nM (50-fold above the EC₅₀). Most importantly, mice werestill healthy after 24 h dCA treatment.

TABLE 1A Hepatic microsomal stability evaluated by incubating 1 μM with0.2-1 mg/ml hepatic microsomes. The reaction is initiated by addingNADPH (1 mM). Aliquots are removed at 0, 5, 10, 20, 40 and 60 minutes.At the end of the assay, the samples are analyzed by LC-MS/MS. Data islog transformed and represented as half-life. Sutinib used forcomparison. a Species (T_(1/2) in minutes) Compound ID Human Mouse dCA60 181 Sunitinib 77 28

TABLE 1B Pharmacokinetics of CA assessed in C57B1-6 mice. Drug levelsmeasured by LC-MS/MS. A 3 mouse mini-PK assessment generatingconcentration vs. time profiles used to aid the design of pharmacologyexperiments. A sample formulation 1 mg/ml CA in water of 10 mg/kg dosedintravenously (IP) via the tail vein and orally by gavage (PO) withblood draws at 1, 6, and 24 hours. b Plasma Concentration Time (hr)Mouse PO (μM) IP (μM) 1 1 0.95 2.19 2 0.78 1.96 3 0.84 3.19 Avg. 0.852.45 6 1 0.34 0.52 2 0.53 0.45 3 0.71 0.9 Avg. 0.52 0.63 24 1 0.03 0.042 0.05 0.03 3 0.06 0.06 Avg. 0.05 0.04

Discussion

From the findings described herein, dCA is the most potent anti-Tatinhibitor described to date. It has exquisite binding selectivity forthe basic domain of HIV Tat, a region also responsible for the Tat-TARinteraction. Importantly, dCA has a drug-like structure, is highlysoluble in water, and displays good bioavailability in mice. dCAinhibits both HIV-1 and HIV-2 replication in tissue culture-adaptedcells or in primary cells when used at single digit nanomolarconcentrations, with no associated toxicity at the cellular level. Eventhough dCA alone fails to totally inhibit acute HIV infections, due toresidual Tat-independent promoter activity, this feature is desirable asit limits off target effects from shared transcription factors bindingcellular and viral promoters, such as NF-κB. Furthermore, dCA actsadditively with other ARVs. HIV-1 lacking Tat undergoes some basaltranscription, however does not sustain a spreading infection.Nonetheless, when chronically infected cells were grown in 100 nM dCAfor longer periods of time, 99% of viral replication was inhibited.

dCA reduces both transcriptional initiation and elongation from theviral promoter, which is consistent with inhibiting the Tat-mediatedconversion of hypophosphorylated RNAPII to the hyperphosphorylated,processive form. Furthermore, termination of dCA treatment does notresult in immediate virus rebound because the HIV promoter istranscriptionally silenced in the absence of Tat activity. This featuremay also be extremely valuable at reducing the emergence of resistantHIV-1 strains.

Tat accumulates in the nucleolus via the basic region but whether itsfunction in this compartment is relevant for pathogenesis is stilldebated. dCA excludes Tat from the nucleolus, most likely because itsassociation with the Tat basic domain inhibits Tat-RNA interactions thatmost likely cause nucleolar accumulation. Whether dCA-mediated nucleolarTat exclusion translates into any significant phenotypic outcome in HIVpathogenesis, other than its effect on transcriptional activity, remainsto be addressed.

In an effort to understand the molecular basis of the only reportedanti-proliferative and anti-migratory activity of CA against HUVECs, ahigh throughput kinome binding assay was performed. CA was reported tobind to CDK11 (K_(d)=10±2 nM), CDK8 (K_(d)=17±2 nM), and ROCK II kinases(K_(d)=220±2 nM), however no inhibition of kinase activity was everdemonstrated. dCA binding to CDK11 was not confirmed. dCA did notinhibit the kinase activity of CDK11 in vitro nor did it bind tobiotinylated dCA. Moreover, inhibition of CDK11 activity would beexpected to be toxic, as CDK11 knockdown severely impairs cellularviability, and at the nanomolar concentrations of CA at which it wasreported to interact with CDK11. Surprisingly, no toxicity was observedin this study.

Low levels of viral production persist in HIV-infected subjects takingHAART and are a major obstacle for complete eradication of theinfection. dCA treatment was extremely successful at reducing viralproduction by a drastic 99.7% from primary CD4⁺ T cells isolated fromaviremic patients who had been under HAART treatment for a long periodof time. Distinct from any currently available ARVs that prevent newrounds of infection, dCA inhibits HIV production from integratedproviral DNA, which by its mode of action may drastically reduce the lowlevels of persistent viremia observed in treated subjects. With atherapeutic index of over 8000, dCA defines a novel class of HIVanti-viral drugs endowed with the ability to decrease residual viremiaduring HAART and should be considered as a promising drug to be includedin therapeutic eradication strategies.

Example 2 Identification of CA-Associated Cellular Proteins

To identify cellular proteins associated with CA, a biotinylated form ofthe compound (Bio-CA) was used. This derivative did not compromise theviability of the cells, and it showed a 10 fold higher EC₅₀ than CA,nevertheless at higher concentration it showed similar efficacy to CA.The Bio-CA was used to cover streptavidin-coated magnetic beads to pulldown interacting proteins from either uninfected or chronically infectedlysates of cells grown in the presence or absence of CA for 48 hours(FIG. 14D). The identity of the proteins pulled down under the differentconditions was determined by HPLC MS/MS analysis. The proteins wereidentified with a greater than 95% confidence using a proprietaryScripps proteomics software package for protein identification,statistical analysis, and mass/peptide sequence correlation. The HIVproteome was added to the proteomics software search database beforeanalysis. Many proteins were identified in uninfected untreated and inchronically untreated samples (approximately 300), however only 53 weredisplaced by more than 50% by the presence of CA. Of these 53 proteins,it appears that at least 2 may have a role in HIV-1 replication:DNA-dependent protein kinase catalytic subunit (DNA-PK) and helicaselike transcription factor (HLTF).

CA binds DNA-PK and Tat, but not a TAR-nonbinding mutant of Tat. UsingBio-CA coupled to magnetic streptavidin beads, it was shown that CAinteracts with Tat-flag transfected into cells but not with a mutant ofTat that no longer binds TAR. CA did not interact with the RNA bindingprotein 9G8, ABCE1 protein (used as a negative control), nor with theCDK11, which had been previously reported to interact with CA in an invitro kinome assay (Cee V J, et al., Angew Chem Int Ed Engl. 2009;48(47):8952-7) (FIG. 15, first 3 rows). DNA-PK seems to interact with CAeither in the presence or absence of Tat or Tat mutant (FIG. 15, 4throw). The P-TEFb complex, CDK9 and Cyclin T1, were also shown tointeract with CA, and an increased association of these two proteinswith CA in the presence of Tat was observed, and a correspondingdecrease in the presence of the Tat mutant; these different bindingaffinities reflect a competition between CA and Tat mutant for P-TEFbbinding, as the Tat mutant does not bind to TAR but it is still capableof binding to P-TEFb. CA was also shown to pull down RNA polymerase,which was expected, as P-TEFb and Tat associate with RNAPII; however aninteraction between CA and Sp1 was not observed. All the associationsbetween CA and the cellular proteins observed might be direct orindirect, and experiments using recombinant proteins are necessary todetermine the nature of these interactions. Altogether, these resultsprovide evidence that Tat-stimulated elongation from the HIV-1 promotermay be one of the mechanisms by which Cortistatin A prevents retroviralreplication.

Assessment of whether CA inhibits DNA-PK phosphorylation of Sp1. DNA-PKwas identified as a binding partner of CA by mass spectrometry andfurther confirmation of this interaction was provided by performing apull down assay (FIG. 15). Without wishing to be bound by theory, it washypothesized that part of the mechanism by which CA inhibits HIVreplication is by blocking the accrued DNA-PK phosphorylation of Sp1mediated by Tat with a consequent reduction in both basal andTat-mediated transcriptional activation of the HIV LTR promoter. Sp1 isthought to be essential for basal transcription and Tat-mediatedactivation of HIV-1. This is concordant with the fact that Sp1 isupregulated in activated T cells, which compose the primary reservoirfor HIV-1 replication. The data so far provides evidence that CA reducesthe transcription activity from CMV and MLV promoters. These resultsindicate that CA acts in a Tat-independent fashion on CMV and MLVpromoters, and one possible explanation would be a reduction in Sp1activity on these promoters (CMV has 11 Sp1 binding sites).

Example 3 Modulation of Neurotoxicity

One of the more notable early events in HIV infection is how rapidly thevirus is detected in the central nervous system (CNS). This may resultin a variety of clinical abnormalities, including HIV-associatedencephalitis (HIVE) and dementia (HAD), which occur in approximately10-15% of patients chronically infected in the United States (A. V.Albright, et al., J. Neurovirol. 9 (2) (2003) 222-227; J. C. McArthur,et al., Lancet Neurol. 4 (9) (2005) 543-555). Despite the initial dropin the incidence of cognitive impairment as a result of highly activeantiretroviral therapy (HAART), CNS disease is again increasing asHIV-infected individuals are living longer.

In the brain, macrophages/microglia are the primary cells infected byHIV, and these cells can support viral replication. A small percentageof astrocytes can also be infected, but HIV entry (B. Schweighardt, etal., AIDS Res. Hum. Retroviruses, 17 (12) (2001) 1133-1142) andreplication (C. L. Ong, et al., J. Virol. 79 (20) (2005) 12763-12772)are inefficient. The contribution of infected astrocytes to CNS diseaseis not well defined. There is no evidence that neurons are infected withthe virus; however, neuronal damage and dropout occur, indicating thatneuronal cell death must be the result of indirect mechanisms, such asneurotoxins released by HIV-infected and uninfected cells. One suchneurotoxin released by infected cells is the transactivator of thevirus, HIV Tat.

HIV Tat, a virally encoded protein that promotes replication, can bereleased by HIV-infected cells to the extracellular space, cerebrospinalfluid (CSF) and sera. Tat has been detected in the brains of people withHIVE by mRNA and Western blotting analyses (L. Hudson, et al., J.Neurovirol. 6 (2) (2000) 145-155; C. A. Wiley, et al., AIDS 10 (8)(1996)843-847). It is unclear whether the majority of the detected tat isreleased by infected cells within the CNS or is specifically transportedacross the blood-brain barrier (BBB) from the sera, but either way tatis taken up by CNS cells with toxic consequences often resulting inapoptosis, particularly in neurons.

Tat is an 86- to 104-amino-acid viral protein that activates humanimmunodeficiency virus type 1 expression, modifies several cellularfunctions, and causes neurotoxicity. Here, the extent was determined asto which peptide fragments of human immunodeficiency virus type 1 BRUTat₁₋₈₆, produced neurotoxicity, increased levels of intracellularcalcium ([Ca²⁺]i), and affected neuronal excitability. Tat₃₁₋₆₁ but notTat₄₈₋₈₅ dose dependently increased cytotoxicity and levels of [Ca²⁺]iin cultured human fetal brain cells. Similarly, Tat₃₁₋₆₁ but notTat₄₈₋₈₅ depolarized rat hippocampal CA1 neurons in slices of rat brain.The neurotoxicity and increases in [Ca²⁺]i could be significantlyinhibited by non-N-methyl-D-aspartate excitatory amino acid receptorantagonists.

Shorter 15-mer peptides which overlapped by 10 amino acids each andwhich represented the entire sequence of Tat₁₋₈₆ failed to produce anymeasurable neurotoxicity. Although it remains to be determined if Tatacts directly on neurons and/or indirectly via glial cells, thesefindings do provide evidence that Tat neurotoxicity is conformationallydependent, that the active site resides within the first exon of Tatbetween residues 31 to 61, and that these effects are mediated at leastin part by excitatory amino acid receptors.

Although the invention has been illustrated and described with respectto one or more implementations, equivalent alterations and modificationswill occur to others skilled in the art upon the reading andunderstanding of this specification and the annexed drawings. Inaddition, while a particular feature of the invention may have beendisclosed with respect to only one of several implementations, suchfeature may be combined with one or more other features of the otherimplementations as may be desired and advantageous for any given orparticular application.

The Abstract of the Disclosure is provided to allow the reader toquickly ascertain the nature of the technical disclosure. It issubmitted with the understanding that it will not be used to interpretor limit the scope or meaning of the following claims.

1. A method of preventing viral infection or treating a viral infectionin a patient, comprising: administering to the patient a therapeuticallyeffective amount of an inhibitor of retroviral transcription wherein theinhibitor inhibits retroviral transcription as compared to a control;and, preventing viral infection or treating a viral infection in thepatient, wherein the inhibitor of retroviral transcription comprisescortistatins, cortistatin derivatives, analogs, substituted cortistatinsor salts thereof.
 2. The method of claim 1, wherein the retroviral viralinfection is a lentivirus.
 3. The method of claim 2, wherein thelentivirus is a human immunodeficiency virus (HIV).
 4. The method ofclaim 1, wherein the inhibitor of retroviral transcription inhibitsfunction or activity of a Trans-Activator of Transcription (Tat), amolecule associated with Trans-Activator of Transcription (Tat), amolecule associated with Transactivation Responsive element (TAR) aTransactivation Responsive element (TAR) and/or interaction between aTrans-Activator of Transcription (Tat) and a Transactivation Responsiveelement (TAR), DNA-PK or combinations thereof. 5-11. (canceled)
 12. Themethod of claim 1, wherein the inhibitor of retroviral transcriptioncomprises a cortistatin agent having a general structure of Formula XII:

Wherein: R¹ is hydrido (H), a straight chain, branched chain or cyclicalkyl, alkenyl, or alkynyl moiety, an aromatic, heterocyclic oralicyclic moiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; R⁵ is hydrido (H), a straight chain, branched chain or cyclicalkyl, alkenyl, or alkynyl moiety, an aromatic, heterocyclic oralicyclic moiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; and the circled X is a cyclic or heterocyclic substituent thatcontains 4 to about 15 carbon atoms, contains one to three saturated orunsaturated rings and up to three atoms per ring that are other thancarbon and can be oxygen, nitrogen or sulfur.
 13. The method of claim 1,wherein the inhibitor of retroviral transcription comprises acortistatin agent having a general structure of Formula XIII:

Wherein: R¹ is hydrido (H), a straight chain, branched chain or cyclicalkyl, alkenyl, or alkynyl moiety, an aromatic, heterocyclic oralicyclic moiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; R⁵ is hydrido (H), a straight chain, branched chain or cyclicalkyl, alkenyl, or alkynyl moiety, an aromatic, heterocyclic oralicyclic moiety that contains one to about 24 carbon atoms, in which aheterocyclic moiety contains 1 to four rings that each contain up tofour ring atoms other than carbon that can be oxygen, nitrogen orsulfur; and the circled X is a cyclic or heterocyclic substituent thatcontains 4 to about 15 carbon atoms, contains one to three saturated orunsaturated rings and up to three atoms per ring that are other thancarbon and can be oxygen, nitrogen or sulfur; with the proviso that R¹and R⁵ are not both methyl when the circled X group is a 7-isoquinoline.14. The method of claim of claim 1, wherein the cortistatin analog is adidehydro-cortistatin A (dCA).
 15. The method of claim 1, wherein thecortistatin is cortistatin A.
 16. The method of claim 1, furthercomprising administering to a patient therapeutically effective amountof one or more anti-retroviral drugs.
 17. The method of claim 16,wherein the antiviral drugs comprise one more of: fusion inhibitors(FIs), nucleoside reverse transcriptase inhibitors (NRTIs),non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleotidereverse transcriptase inhibitors (NtRTIs), protease inhibitors (PIs) orintegrase inhibitors (INIs).
 18. A method of inhibiting retroviralproduction in vitro or in vivo comprising: contacting a cell oradministering to a patient an effective amount of an inhibitor ofretroviral replication; and modulating retroviral replication in vitroor in vivo, wherein the inhibitor of retroviral transcription comprisescortistatins cortistatin derivatives, analogs, substituted cortistatinsor salts thereof.
 19. The method of claim 18, wherein the retrovirus isa human immunodeficiency virus (HIV).
 20. The method of claim 18,wherein the inhibitor of retroviral transcription inhibits function oractivity of a Trans-Activator of Transcription (Tat), a moleculeassociated with Trans-Activator of Transcription (Tat), a moleculeassociated with Transactivation Responsive element (TAR) aTransactivation Responsive element (TAR) and/or interaction between aTrans-Activator of Transcription (Tat) and a Transactivation Responsiveelement (TAR), DNA-PK or combinations thereof.
 21. The method of claim18, optionally comprising contacting a cell or administering to apatient infected with a retrovirus a therapeutically effective amount ofone or more anti-retroviral drugs.
 22. The method of claim 21, whereinthe anti-retroviral drugs comprise one more of: fusion inhibitors (FIs),nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleosidereverse transcriptase inhibitors (NNRTIs), nucleotide reversetranscriptase inhibitors (NtRTIs), protease inhibitors (PIs) or imegraseinhibitors (INIs).
 23. (canceled)
 24. The method of claim of claim 18,wherein the cortistatin analog is a didehydro-cortistatin A (dCA). 25.The method of claim 18, wherein the cortistatin is cortistatin A.
 26. Amethod of modulating function or activity of a human immunodeficiencyvirus (HIV) transcriptional promoter in vitro or in vivo comprising:administering a therapeutically effective amount of an agent whichmodulates function or activity of a Trans-Activator of Transcription(Tat), a molecule associated with Trans-Activator of Transcription(Tat), a molecule associated with Transactivation Responsive element(TAR) a Transactivation Responsive element (TAR) and/or interactionbetween a Trans-Activator of Transcription (Tat) and a TransactivationResponsive element (TAR), or DNA-PK; and, modulating function oractivity of a human immunodeficiency virus (HIV) transcriptionalpromoter in vitro or in vivo.
 27. The method of claim 26, wherein theagent comprises cortistatin, cortistatin derivatives, analogs,substituted cortistatins or salts thereof.
 28. A pharmaceuticalcomposition comprising: cortistatins, cortistatin derivatives, analogs,substituted cortistatins or salts thereof.
 29. (canceled)